Package: a4 Version: 1.57.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db License: GPL-3 MD5sum: 12a1bf82a4a6ec53bef4e9070a5df561 Package: a4Base Version: 1.57.0 Depends: a4Preproc, a4Core Imports: methods, graphics, grid, Biobase, annaffy, mpm, genefilter, limma, multtest, glmnet, gplots Suggests: Cairo, ALL, hgu95av2.db, nlcv Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 82ed248ce21ef5de6f2f23ff1d80122c Package: a4Classif Version: 1.57.0 Depends: a4Core, a4Preproc Imports: methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils, graphics, stats Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: c855750d75774263b116a99f34a054c3 Package: a4Core Version: 1.57.0 Imports: Biobase, glmnet, methods, stats Suggests: knitr, rmarkdown License: GPL-3 MD5sum: c0ffd42571c26caa5f1fbe747c2a85e0 Package: a4Preproc Version: 1.57.0 Imports: BiocGenerics, Biobase Suggests: ALL, hgu95av2.db, knitr, rmarkdown 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Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr, BiocStyle License: Apache License (== 2.0) + file LICENSE MD5sum: 58a430f9b08a484856b92496a491ca94 Package: AMOUNTAIN Version: 1.35.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: 0a146fa802070dedf84888f7f934c419 Package: Anaquin Version: 2.33.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 721d2629e08d7e5cc15588cd3cff198f Package: ANCOMBC Version: 2.11.1 Depends: R (>= 4.5.0) Imports: stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils Suggests: mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: 5571f24fcadf02f76416c58bbbaa7429 Package: ANF Version: 1.31.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: c20ad1611a8280e9c2c78d221aef7828 Package: animalcules Version: 1.25.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 8f17d7bcf8762c2be76f068da6c326ac Package: annaffy Version: 1.81.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 00be4b544000150eb85ef2dbdcc422c9 Package: annmap Version: 1.51.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: d7c8a9ef6967cf61ca893f0dac452330 Package: annotate Version: 1.87.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 271dd2703623e3d4727dece58bff080e Package: AnnotationDbi Version: 1.71.1 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: b138dc22ce2f89b4d9e85ceb223770f0 Package: AnnotationFilter Version: 1.33.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: f9aa5d807cfa9daaada90874229549b3 Package: AnnotationForge Version: 1.51.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: 4297ef2f2da3ee58b102889bce6ad8a1 Package: AnnotationHub Version: 3.99.6 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.3) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr2, yaml, dplyr, BiocBaseUtils Suggests: IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 19e0052665f9093cfcf95c9e75539822 Package: AnnotationHubData Version: 1.39.2 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, Seqinfo, GenomeInfoDb (>= 1.45.5), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 91951ac04cf3360dfd2681b79ecdf6ff Package: annotationTools Version: 1.83.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: f453313f7e277048223d812f3fd616b7 Package: anota Version: 1.57.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 9a5050f2bed4add539c9f7517607bb9a Package: anota2seq Version: 1.31.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: a7b05aa5e0782d10077424d737f16ddc Package: antiProfiles Version: 1.49.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) 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jsonlite, rlang, tibble, tidyr, utils, methods, plyr, stringr Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 4569b28e1bb080dbc6b006880db476bd Package: apComplex Version: 2.75.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 9e936a684d40664b7d6c856d3fcfc913 Package: apeglm Version: 1.31.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: c87c9dd6c04183f8c3ce38abd94e969a Package: APL Version: 1.13.0 Depends: R (>= 4.4.0) Imports: Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly, SeuratObject, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, sparseMatrixStats, testthat License: GPL (>= 3) MD5sum: 78b12636412573a6f50f93b385ae2015 Package: 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MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: a36256dd8fe7e63bd95d2f56e1d3ae05 Package: ASAFE Version: 1.35.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 1554e1b2fddaaf934e6728ff4623e621 Package: ASEB Version: 1.53.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 24798926c1b60f03862702e4b5a492e4 Package: ASGSCA Version: 1.43.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 5419b4ca3c4b74fe79b32262dd60f93f Package: ASICS Version: 2.25.0 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: 3c84d580b9920925ee69fb3b5a28b3cc Package: ASpli Version: 2.19.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply, txdbmaker License: GPL MD5sum: b7d1c9b607c73c1e94a75658cf0ab7c2 Package: AssessORF Version: 1.27.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: 84c568b03d434efe35bb5912636d8935 Package: ASSET Version: 2.27.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: cbe228e3f138f61b4fdccd5a90e0e469 Package: ASSIGN Version: 1.45.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8e3cecc0112fa943910fba42d1627a4f Package: assorthead Version: 1.3.11 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: d64bf3afaaa89b2157ec65b30fc3ca26 Package: ASURAT Version: 1.13.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 3a92cb8b041b1796549c0e07f91c31c0 Package: ATACseqQC Version: 1.33.1 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 72976ffb0e9978c448b3e72eb402f4ff Package: ATACseqTFEA Version: 1.11.1 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, Seqinfo, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: 23f5b2e95156dc4d18cca6b35c87e991 Package: atena Version: 1.15.2 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, Seqinfo, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: 5a5c6d1f00480761b519cf57ccc112f3 Package: atSNP Version: 1.25.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: cc9b2027154911fcf75f173dc568150e Package: attract Version: 1.61.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: f84c8ae4b06e03b02921040af6f8c58c Package: AUCell Version: 1.31.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 2dfc47e4c0d8f54572a987ff87680bc6 Package: autonomics Version: 1.17.16 Depends: R (>= 4.0) Imports: abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, lme4, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, survival, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite, knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: 8e0bbf0f1ee182821d480a5be95b552a Package: AWAggregator Version: 0.99.4 Depends: R (>= 4.5.0) Imports: dplyr, Peptides, progress, purrr, ranger, rlang, stats, stringr, tidyr, toOrdinal, utils Suggests: AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9468013df5c2ef1f4a194fa53ed167ae Package: AWFisher Version: 1.23.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 654e288ba2feea0cb1ed96de5790c837 Package: awst Version: 1.17.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: dbe3c637da4c9c70bc1121e3c2d4002c Package: BaalChIP Version: 1.35.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 8238738f3a13dd078a96541c2445cf3f Package: bacon Version: 1.37.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 868053d4da5e8f69425786a874f58bf7 Package: BADER Version: 1.47.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 873c286936db152c566821cf0facfec0 Package: BadRegionFinder Version: 1.37.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: e074dff07dd1be46114e1dd81b925bca Package: BAGS Version: 2.49.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: da01c779a8e1aee80fa513adbb66c1c0 Package: ballgown Version: 2.41.1 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), Seqinfo Suggests: testthat, knitr, markdown License: Artistic-2.0 MD5sum: f3e3af3a208ba986bea18d48e1454ff3 Package: bambu Version: 3.11.2 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: b424e71d687e2644ccdcc6b120408e38 Package: bamsignals Version: 1.41.2 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges LinkingTo: Rcpp, Rhtslib (>= 1.13.1) Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 326f49d0a7bb35adbbf3090dcf622aa5 Package: BANDITS Version: 1.25.1 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 62eb05c56179287431a931cacea1471c Package: bandle Version: 1.13.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4) LinkingTo: Rcpp, RcppArmadillo, BH Suggests: testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 643a89109decea204d8452a2f46b7758 Package: Banksy Version: 1.5.8 Depends: R (>= 4.4.0) Imports: aricode, BiocParallel, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, Matrix, MatrixGenerics, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE MD5sum: 723d2bd21b061409feb1c6da1297d398 Package: banocc Version: 1.33.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: d4f2523c448e362438366286aad133aa Package: barbieQ Version: 1.1.2 Depends: R (>= 4.5) Imports: magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap, ggplot2, logistf, limma, stats, igraph, utils, data.table, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 68690214287fd0fb97df4104cf1502a3 Package: basecallQC Version: 1.33.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: beace5489196913f522eb1ef3596889b Package: BaseSpaceR Version: 1.53.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 44d38277e80636b2627ba1e3afe3aee7 Package: Basic4Cseq Version: 1.45.1 Depends: R (>= 3.5.0), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: fc8f6815a61dffb542f5e83570af2fe8 Package: BASiCS Version: 2.21.1 Depends: R (>= 4.1), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick License: GPL-3 MD5sum: 1309c478147506f3cc15cab30a70fa6b Package: BASiCStan Version: 1.11.0 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: 7347460b67c8cfd7c6ada198c8864c8c Package: BasicSTARRseq Version: 1.37.1 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,Seqinfo,stats Suggests: knitr License: LGPL-3 MD5sum: c2bc479cf164911a349da7c8e3c15d6d Package: basilisk Version: 1.21.5 Depends: reticulate Imports: utils, methods, parallel, dir.expiry Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: ecfb23a2be0f6fde6f4800e167143e3a Package: basilisk.utils Version: 1.21.2 Imports: utils, methods, tools, dir.expiry Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 1e8fdb555fd7dc800df34a368073cb84 Package: batchCorr Version: 0.99.8 Depends: R (>= 4.4.0), SummarizedExperiment Imports: reshape, mclust, BiocParallel, methods Suggests: BiocStyle, knitr, testthat License: GPL-2 MD5sum: a7fb1237f119167a43e5b70ea327b9a1 Package: batchelor Version: 1.25.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: efafcd082499a1b0abf2e53505f3cb89 Package: BatchQC Version: 2.5.13 Depends: R (>= 4.5.0) Imports: data.table, DESeq2, dplyr, EBSeq, edgeR, FNN, ggdendro, ggnewscale, ggplot2, limma, matrixStats, methods, MASS, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, shinyjs, shinythemes, stats, SummarizedExperiment, sva, S4Vectors, tibble, tidyr, tidyverse, umap, utils Suggests: BiocManager, BiocStyle, bladderbatch, curatedTBData, devtools, knitr, lintr, MultiAssayExperiment, plotly, rmarkdown, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1d1b0cd530eebbcba18c7e6433e7527f Package: BatchSVG Version: 1.1.1 Depends: R (>= 4.5.0) Imports: scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2, RColorBrewer, scales, SummarizedExperiment Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD License: Artistic-2.0 MD5sum: 0ec7d3d3d9b9886ced78c3acb741889d Package: BayesKnockdown Version: 1.35.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: 83306f16738fc5ab5952ae2e4a9fe58e Package: BayesSpace Version: 1.19.4 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, magrittr, assertthat, arrow, mclust, RCurl, DirichletReg, xgboost (< 2.0.0), utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr, scales, microbenchmark, BiocFileCache, BiocSingular, BiocParallel LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: bdb9f7fb8a9ddac4cf24564a860ba5fe Package: bayNorm Version: 1.27.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 75db2daaedcf34e9d6a9fa323a89b6b6 Package: baySeq Version: 2.43.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 5aaa3f1d3cd4876f799f20af55ed2e58 Package: BBCAnalyzer Version: 1.39.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 92cf6ca63c82fc46f8e33d0d0d6c2b48 Package: BCRANK Version: 1.71.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 7e66b97819219b283e83f03ec92937c4 Package: bcSeq Version: 1.31.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: 0889b91d54cd8f421c2cf37cd8fdd5b6 Package: beachmat Version: 2.25.5 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp, assorthead (>= 1.3.3) Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 License: GPL-3 MD5sum: 3514faa19466bbcf50df3b08a4ca9e28 Package: beachmat.hdf5 Version: 1.7.2 Imports: methods, beachmat, HDF5Array, DelayedArray, Rcpp LinkingTo: Rcpp, assorthead, beachmat, Rhdf5lib Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix License: GPL-3 MD5sum: 4069afaaae0de1b319840eb39f72256b Package: beachmat.tiledb Version: 1.1.1 Imports: methods, beachmat, tiledb, TileDBArray, DelayedArray, Rcpp LinkingTo: Rcpp, assorthead, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix License: GPL-3 MD5sum: 3c7e2ff39066cc2b517d7feb0d09348d Package: BeadDataPackR Version: 1.61.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: 0363af34008f9175b5b9330faf33ab3f Package: BEAT Version: 1.47.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: 5ecb86d5359ab58f011e55f464a64d52 Package: BEclear Version: 2.25.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 MD5sum: 3b9d52d9fc04030a8191a0d5facc6a6b Package: beer Version: 1.13.0 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: d302c49ab822644bd5f36a3352f45a99 Package: BERT Version: 1.5.0 Depends: R (>= 4.3.0) Imports: cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>= 0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 307d4a33d4dc14a94bd8f7f0c5ed1c57 Package: betaHMM Version: 1.5.1 Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: d426085f050e6212ee49289f4acb8ff9 Package: bettr Version: 1.5.4 Depends: R (>= 4.4.0) Imports: dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6), tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid, methods, cowplot, Hmisc, sortable, shinyjqui, grDevices, scales, DT, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 69cf3b3a77a40c8d47a478b18a19d849 Package: BG2 Version: 1.9.0 Depends: R (>= 4.2.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 5a27eaba677e78b7bd5e3643a5166416 Package: BgeeCall Version: 1.25.0 Depends: R (>= 3.6) Imports: AnnotationDbi, curl, ggplot2, scales, GenomicFeatures, tximport, Biostrings, readr, sjmisc, RCurl, RSQLite, tools, stringr, rtracklayer, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker, IRanges, spatstat.univar Suggests: knitr, testthat, rmarkdown, AnnotationHub, GenomeInfoDb, httr License: GPL-3 + file LICENSE MD5sum: 3ad6db90e1270954e0d06a41ed455745 Package: BgeeDB Version: 2.35.1 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata, HDF5Array, bread Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: 8d2cad375628613cbe6a47eb8b64ffe8 Package: bgx Version: 1.75.1 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Imports: Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: affydata, hgu95av2cdf License: GPL-2 MD5sum: 9a65ce208f6cca05926568d7c20addda Package: BicARE Version: 1.67.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db Imports: methods Suggests: hgu95av2 License: GPL-2 MD5sum: 7ad9136b63ed0dbfb5802e1507d33fa9 Package: BiFET Version: 1.29.1 Depends: R (>= 3.5.0) Imports: stats, poibin, GenomicRanges Suggests: rmarkdown, testthat, knitr License: GPL-3 MD5sum: 267155b7c0563323e01e311042189b69 Package: bigmelon Version: 1.35.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: e6953eae3b0b7270476b6eee395d7a81 Package: BindingSiteFinder Version: 2.7.1 Depends: GenomicRanges, R (>= 4.2) Imports: tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap, RColorBrewer, lifecycle, rlang, forcats, dplyr, GenomicFeatures, IRanges, kableExtra, ggdist Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr, txdbmaker, ggrepel, stringr License: Artistic-2.0 MD5sum: bbda650c789ccddb425163f2254411de Package: Biobase Version: 2.69.1 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma License: Artistic-2.0 MD5sum: 9d34d45756221e6a4fe2636720d77028 Package: biobroom Version: 1.41.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment License: LGPL MD5sum: 25b02de5c3f8653b03335daa327c30f7 Package: Bioc.gff Version: 0.99.17 Depends: R (>= 4.5.0) Imports: BiocBaseUtils, BiocGenerics, BiocIO, curl, GenomicRanges, IRanges, methods, Rsamtools, S4Vectors, Seqinfo, stats, utils, XVector LinkingTo: S4Vectors, XVector, IRanges Suggests: BiocFileCache, BiocStyle, GenomicFeatures, GenomeInfoDbData, knitr, httr2, rmarkdown, rvest, tinytest, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: ba8514276600e1147eb7d74771935829 Package: bioCancer Version: 1.37.0 Depends: R (>= 4.1.0), radiant.data (>= 0.9.1), cBioPortalData, XML (>= 3.98) Imports: R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, AnnotationDbi, shinythemes, Biobase, geNetClassifier, org.Hs.eg.db, org.Bt.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr, tibble, GO.db Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE MD5sum: cbde23c7663043bdbb5a05e3215ca4b8 Package: BioCartaImage Version: 1.7.0 Depends: R (>= 4.3.0) Imports: magick, grid, stats, grDevices, utils Suggests: testthat, knitr, 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dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), AnnotationDbi, VariantAnnotation (>= 1.55.1), ensembldb (>= 2.33.1), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: 72e82818056af75908adca1b95f5a7aa Package: BiRewire Version: 3.41.0 Depends: igraph, slam, Rtsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 9703736259bd8a41e166d49241f047ad Package: BiSeq Version: 1.49.1 Depends: R (>= 3.5.0), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, Seqinfo, GenomicRanges, SummarizedExperiment, rtracklayer, 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Version: 2.19.3 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: 33c18438409c9253114b7a7935365bbc Package: BrowserViz Version: 2.31.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 384e21fe813042a6622fe9d3f15a5140 Package: BSgenome Version: 1.77.2 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2), BiocIO, rtracklayer (>= 1.69.1) Imports: utils, stats, matrixStats, XVector, Rsamtools (>= 2.25.1) Suggests: BiocManager, GenomeInfoDb, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, 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permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5, beachmat (>= 2.23.2) LinkingTo: Rcpp, beachmat, assorthead (>= 1.1.4) Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, batchtools License: Artistic-2.0 MD5sum: 2c9e3a4a96e74df9db719b28ccd00d9c Package: BufferedMatrix Version: 1.73.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: c4c126957956a99cc71b27f151f5b6d9 Package: BufferedMatrixMethods Version: 1.73.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: a74797aef30f3a500968dd7acc5868ff Package: bugsigdbr Version: 1.15.3 Depends: R (>= 4.1) Imports: BiocFileCache, methods, vroom, utils Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1b41754088ef4ad2c29ca6936fc67762 Package: BulkSignalR Version: 1.1.5 Depends: R (>= 4.5) Imports: BiocFileCache, httr2, RCurl, cli, curl, rlang, jsonlite, matrixStats, methods, doParallel, glmnet, ggalluvial, ggplot2, gridExtra, grid, Rtsne, ggrepel, foreach, multtest, igraph, orthogene, stabledist, circlize (>= 0.4.14), ComplexHeatmap (>= 2.0.0), stats, scales, RANN, SpatialExperiment, SummarizedExperiment, tools Suggests: knitr, markdown, rmarkdown, STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme License: CeCILL | file LICENSE MD5sum: 2ca3cc4511ec8697eed220c31c3f3dbd Package: BUMHMM Version: 1.33.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: 610168f08aeaaa904595c4f360962ca4 Package: bumphunter Version: 1.51.1 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), Seqinfo, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, GenomeInfoDb, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 493d3e3bb32c25f5ba3c1ae48ff6576f Package: BumpyMatrix Version: 1.17.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 66b31b2189171344f4da99556f56af75 Package: BUS Version: 1.65.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: 44785c96da996faba26ec172d5944b5c Package: BUScorrect Version: 1.27.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ff880ebe150499b3d69033550fa74a67 Package: BUSpaRse Version: 1.23.2 Depends: R (>= 3.6) Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, biomaRt, BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, lifecycle, magrittr, Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: 7d12e26bc4ccf3895cdb94000ce0b108 Package: BUSseq Version: 1.15.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: cc3651df86ddfdbba46ab874afbdeff3 Package: CAEN Version: 1.17.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle License: GPL-2 MD5sum: 08ea164935f1bfb2b2f82d135d080007 Package: CAFE Version: 1.45.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 2e0e4f5b62b976d3c6bd5fc43ecd7194 Package: CAGEfightR Version: 1.29.1 Depends: R (>= 3.5), GenomicRanges (>= 1.61.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 1.39.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), Seqinfo, GenomicFeatures(>= 1.61.4), GenomicAlignments(>= 1.45.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: a5d2dab5326a5cd7f32fd23b6486d386 Package: cageminer Version: 1.15.2 Depends: R (>= 4.1) Imports: ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: b78512e4d42093a92254d6051103f7b2 Package: CAGEr Version: 2.15.1 Depends: methods, MultiAssayExperiment, R (>= 4.1.0) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR, data.table, formula.tools, Seqinfo, GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr, rlang, Rsamtools (>= 2.25.1), reshape2, rtracklayer (>= 1.69.1), S4Vectors (>= 0.27.5), scales, som, stringdist, stringi, SummarizedExperiment (>= 1.39.1), utils, vegan, VGAM Suggests: BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 60cf6abaa20b68749a6fa4fd47a295c3 Package: calm Version: 1.23.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 18ba6becdcc1894aaaf4bda830b1a857 Package: CaMutQC Version: 1.5.5 Depends: R (>= 4.5.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle, shiny License: GPL-3 MD5sum: ae787b07482dd842a02654c8550931c7 Package: canceR Version: 1.43.0 Depends: R (>= 4.3), tcltk, cBioPortalData Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3 Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 5087acf079ab573cf2a4889f0e9009a0 Package: cancerclass Version: 1.53.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 54fe123fe4eb4ec7c81bea79006ebe4b Package: cardelino Version: 1.11.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: 49685be591d86721b87b12c5f94e7f70 Package: Cardinal Version: 3.11.0 Depends: R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics, S4Vectors, methods, stats, stats4 Imports: CardinalIO, Biobase, EBImage, graphics, grDevices, irlba, Matrix, matter (>= 2.7.10), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 911b885ec3e838a233cc540842cbe7a6 Package: CardinalIO Version: 1.7.0 Depends: R (>= 4.4), BiocParallel, matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 32e78698a0f7d081ed2ac1347a22ef6e Package: CARDspa Version: 1.1.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.7),RcppArmadillo, SummarizedExperiment, methods, MCMCpack, fields, wrMisc, concaveman, sp, dplyr, sf, Matrix, RANN, ggplot2, reshape2, RColorBrewer, S4Vectors, scatterpie, grDevices,ggcorrplot, stats, nnls, BiocParallel, RcppML, NMF, spatstat.random, gtools, SingleCellExperiment, SpatialExperiment LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 + file LICENSE MD5sum: 536c556cb23196c6b5cbded8ca36121a Package: CARNIVAL Version: 2.19.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 MD5sum: 323bdcf6ccca8d739c931861d8942380 Package: CATALYST Version: 1.33.1 Depends: R (>= 4.5), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: f804f300317c66a39bf2f5bcc89b82c3 Package: Category Version: 2.75.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: f6fdad85600077003a1c0add9afe382e Package: categoryCompare Version: 1.53.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 MD5sum: 15a633344c3ac45a6579a39c0584bfd3 Package: CausalR Version: 1.41.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 020b9309e40e5ac37c1cf66720fa6114 Package: cbaf Version: 1.31.0 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx, zip Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 952857cc0e5ed9ba60688502acacb788 Package: cBioPortalData Version: 2.21.5 Depends: R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment Imports: BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, Seqinfo, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 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(>= 3.0.0), rmarkdown, markdown, knitr, tidyverse, DescTools, cowplot, BiocStyle, GenomicRanges, SummarizedExperiment, S4Vectors, IRanges License: GPL-3 MD5sum: 5d1e70127a097ca6b82bae44aec4ad7e Package: ccImpute Version: 1.11.0 Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter License: GPL-3 MD5sum: f3648473fe46f8f445b7933ef7d2ffa9 Package: CCPlotR Version: 1.7.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 42038482a4682972a772f102a4919797 Package: CCPROMISE Version: 1.35.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 4a6529ab4ffbce0a1bbe190da4bdd084 Package: ccrepe Version: 1.45.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE MD5sum: e6143f4ca46d4387f5d64a1256c86f01 Package: CDI Version: 1.7.0 Depends: R(>= 3.6) Imports: matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE MD5sum: 6d9b4e481d58453d5c0fa155521d07e0 Package: celda Version: 1.25.0 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize, dendextend, ggdendro, pROC LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 64f7c980c1a7b4b61af668831cea4e76 Package: CellBarcode Version: 1.15.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: 30d8876f137d73099393f8b131523724 Package: cellbaseR Version: 1.33.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: ec7629d6ae880683f04f89a82da4a540 Package: CellBench Version: 1.25.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: a35539bef49db809403a310f73bf998e Package: CelliD Version: 1.17.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: c068e76b74c60f59f2431995c0570cbe Package: cellity Version: 1.37.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 5d6f8608c88e6ebf9d21ccf238c25676 Package: CellMapper Version: 1.35.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: f130da7ff40be27c4bab506d329b7f71 Package: cellmig Version: 0.99.16 Depends: R (>= 4.5.0) Imports: base, ggplot2, ggforce, ggtree, patchwork, ape, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, utils, scales LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat License: GPL-3 + file LICENSE MD5sum: 6dc5fd620c7146b3c31b65169d54defb Package: cellmigRation Version: 1.17.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: e8ee561c314a53d051d1a68a7c9cbb22 Package: CellMixS Version: 1.25.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: f683044d3a6c43271b8d690090b70843 Package: CellNOptR Version: 1.55.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: fb9968e7aa0090cda910d7a6ededf90d Package: cellscape Version: 1.33.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 0d2871da1e673d76ca941b7f17e0255e Package: CellTrails Version: 1.27.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 1f4edf8dd26751d70829759189a24e1c Package: cellxgenedp Version: 1.13.1 Depends: R (>= 4.1.0), dplyr Imports: httr, curl, utils, tools, cli, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: 176a8549729ba822c077ec4e6b589307 Package: censcyt Version: 1.17.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: 758a160d7e42ad6bbf454ab8ad30ce5d Package: Cepo Version: 1.15.0 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE MD5sum: 4d01f2d518e9cb32de9f5d07c6b1d118 Package: ceRNAnetsim Version: 1.21.1 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 67ede66e5f5b3ec36337a6e3e3b3e14c Package: CeTF Version: 1.21.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: 7e016b3d339a07f42e4f1a49ceff0125 Package: CexoR Version: 1.47.1 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, Seqinfo, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 0a8525021534668567d2d67894c62c95 Package: CFAssay Version: 1.43.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: d95d217ab4fef114bae3a97562e35d4d Package: cfdnakit Version: 1.7.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang Suggests: rmarkdown, knitr, roxygen2, BiocStyle License: GPL-3 MD5sum: b970d14940dd3a929ff54d19c3f7bc37 Package: cfDNAPro Version: 1.15.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: b0228300cc14f87524059a271e5994f8 Package: CGHbase Version: 1.69.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: 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prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: 44ae7d618dba5168a7510ac438d0dc0b Package: ChemmineR Version: 3.61.2 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex,codetools Enhances: ChemmineOB License: Artistic-2.0 MD5sum: d9667ff0135f2c28a2038e1f983a163d Package: CHETAH Version: 1.25.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: 345ef0f19e7d1654955c1e2b62ca0249 Package: chevreulProcess Version: 1.1.2 Depends: R (>= 4.5.0), SingleCellExperiment, scater Imports: batchelor, bluster, circlize, cluster, DBI, dplyr, EnsDb.Hsapiens.v86, ensembldb, fs, GenomicFeatures, glue, megadepth, methods, purrr, RSQLite, S4Vectors, scran, scuttle, stringr, tibble, tidyr, tidyselect, utils Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 13a60f83c4de572703159aff03769054 Package: Chicago Version: 1.37.1 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: 5a4564e3deb464b92d91846313576307 Package: chihaya Version: 1.9.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: d35723e421e820f4c43a9e9ed9550c3c Package: chimeraviz Version: 1.35.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: b5db48eaba54c0f5599c505b0e0940b1 Package: ChIPanalyser Version: 1.31.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 0eb9a9e8d702fdffbc38bc7a06e915e4 Package: ChIPComp Version: 1.39.1 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,Seqinfo,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: 832fc489a99bdaa7d1e6aac06d884d48 Package: chipenrich Version: 2.33.1 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, Seqinfo, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 2fe4c8a3f01ad6e69410b71e192f9372 Package: ChIPexoQual Version: 1.33.1 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.45.1) Imports: methods, utils, Seqinfo, stats, BiocParallel, GenomicRanges (>= 1.61.1), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 2.25.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: f9d60120c8a538f3b051febbc925d79e Package: ChIPpeakAnno Version: 3.43.1 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache License: GPL (>= 2) MD5sum: 9481679c69cd02f63cee097f20efe9a2 Package: ChIPseeker Version: 1.45.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, magrittr, methods, plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, yulab.utils (>= 0.1.5) Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat License: Artistic-2.0 MD5sum: 9fada587e3017374e23cac36d9d6232e Package: chipseq Version: 1.59.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 MD5sum: cc1989ba0c16e66812127b89b4dc934c Package: ChIPseqR Version: 1.63.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: bd6041077c5f99f0f4f2fcdb8bdd9d6d Package: ChIPsim Version: 1.63.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 110699d7ad74bcf8af6579a5abddfab5 Package: ChIPXpress Version: 1.53.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 54d782276212b3a886c7356eb42164ac Package: Chromatograms Version: 0.99.6 Depends: BiocParallel, ProtGenerics (>= 1.39.2), R (>= 4.5.0) Imports: methods, S4Vectors, MsCoreUtils (>= 1.7.5), Spectra Suggests: msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), testthat, knitr (>= 1.1.0), rmarkdown, mzR (>= 2.41.4), MsBackendMetaboLights (>= 1.3.1), vdiffr, RColorBrewer License: Artistic-2.0 MD5sum: a67111028ce82f981267277c7f7720f5 Package: chromDraw Version: 2.39.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: dab2601cb7f8a76cc8c84c36bf4ae45b Package: ChromHeatMap Version: 1.63.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: d242829a975ad8d25fdcd56ed51100c1 Package: chromPlot Version: 1.37.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 777b244ba4d3a2c54ce44c8f066cdd73 Package: ChromSCape Version: 1.19.1 Depends: R (>= 4.1) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 MD5sum: bb0527df96300d76e01fee2e6b3c2fc3 Package: chromVAR Version: 1.31.1 Depends: R (>= 3.5.0) Imports: IRanges, Seqinfo, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: ce3c467534fea42743dd4167c66c3b83 Package: cicero Version: 1.27.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: 217c5e14df0751f23470704cf37b1eb4 Package: CIMICE Version: 1.17.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 MD5sum: 6412d16a3d391feb65bcf5bb3c66fdb8 Package: CINdex Version: 1.37.2 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, Seqinfo,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils License: GPL (>= 2) MD5sum: fd5083aee3c789130a62d307b98cb516 Package: circRNAprofiler Version: 1.23.1 Depends: R(>= 4.5.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: 8794bf11e181dd791ac9eda45fbe5876 Package: CircSeqAlignTk Version: 1.11.2 Depends: R (>= 4.2) Imports: stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 76799735f068930ef141442ee0d753f3 Package: CiteFuse Version: 1.21.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: 2d2102c41d3e4b6f5a5672b664c92485 Package: ClassifyR Version: 3.13.8 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale, TOP, BiocNeighbors License: GPL-3 MD5sum: a45433f8d3be42a63081f844b1644f8a Package: cleanUpdTSeq Version: 1.47.1 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: b8082be24f3265f4834fd001af500898 Package: CleanUpRNAseq Version: 1.3.2 Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, Seqinfo, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, KernSmooth, limma, methods, pheatmap, qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2, SummarizedExperiment, stats, tximport, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 288793c951495d279a21a3ec202db2a5 Package: cleaver Version: 1.47.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: 3cf447b5902a8d44a859dce894416d05 Package: clevRvis Version: 1.9.0 Imports: shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 4b626997b90dc39893ddade38030d720 Package: clippda Version: 1.59.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 5b3407a2baefa2f50311ab71bee472e7 Package: clipper Version: 1.49.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: 557c925bed45fbdd6bf77bbbae250463 Package: cliProfiler Version: 1.15.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: ccaaebf90510e4163dd389f90ee04034 Package: cliqueMS Version: 1.23.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop, slam, matrixStats, methods LinkingTo: Rcpp, BH, RcppArmadillo Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA License: GPL (>= 2) MD5sum: 6d0a202fd3a1759debf9d94eec4645a9 Package: Clomial Version: 1.45.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: 819e908e4ee6441eacccb9a7153a5568 Package: clst Version: 1.57.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: 8341aa636bcfd6af93781e1096e96900 Package: clstutils Version: 1.57.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 MD5sum: 43eac3aa6d0c7b4c978d4f46d3ee273a Package: ClustAll Version: 1.5.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: e9973838853c6883b1d464fe79ad5755 Package: clustComp Version: 1.37.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 5e28ade8717138fd1e5b17f84e060b18 Package: clusterExperiment Version: 2.29.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: 7b5ddd523f1c300e18b8cf4e8ea3abe0 Package: ClusterFoldSimilarity Version: 1.5.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: 3119f9dc1e2ff362b94f9f4c90dfb46c Package: ClusterJudge Version: 1.31.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 06434969c8a749979b8e1f7832b1e5fa Package: clusterProfiler Version: 4.17.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.1.6) Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat License: Artistic-2.0 MD5sum: 721ac531850892e495afe1708d0eaafd Package: clusterSeq Version: 1.33.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 6b9e31591a29e7055c2091a6c6a20994 Package: ClusterSignificance Version: 1.37.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 26b38544e6825e9ce1464b350ab24d51 Package: clusterStab Version: 1.81.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: 1a40fdb9c48105c41caf8cadcefd4cc4 Package: clustifyr Version: 1.21.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: 3eeb581022d1039911fdb62c0f4d306d Package: ClustIRR Version: 1.7.9 Depends: R (>= 4.3.0) Imports: blaster, future, future.apply, grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: 18d371df7924045cef99ba324a849b85 Package: clustSIGNAL Version: 1.1.0 Depends: R (>= 4.4.0), SpatialExperiment Imports: BiocParallel, BiocNeighbors, bluster (>= 1.16.0), scater, harmony, SingleCellExperiment, SummarizedExperiment, methods, Matrix, reshape2 Suggests: knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2, patchwork, dplyr, scattermore License: GPL-2 MD5sum: a2bc05e9b2a9e6a82a1df09f79e2c1f5 Package: CMA Version: 1.67.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: d60324de7d03ffa5c35a5eed3c655c6e Package: cmapR Version: 1.21.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE MD5sum: 6bbf4d458b4edf0af8d99e5f300ce2e3 Package: cn.farms Version: 1.57.2 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice License: LGPL (>= 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20bd9ec306fc6310043cd592b162305c Package: CNORode Version: 1.51.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 MD5sum: d780022260557590c037eb2fe9fe11f9 Package: CNTools Version: 1.65.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: 861ba70346ceb44f08e5fa8ad734cd3e Package: CNVfilteR Version: 1.23.0 Depends: R (>= 4.3) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown License: Artistic-2.0 MD5sum: 03721b82cb74d793301158f53ff95528 Package: cnvGSA Version: 1.53.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 8ceec789dad79c66b82489427d6dc8bb Package: CNViz Version: 1.17.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: d1e3a845020764a32d0501b28a4b2ea1 Package: CNVMetrics Version: 1.13.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: f26dc07fe060b281305c31d2afe871a7 Package: CNVPanelizer Version: 1.41.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: 6b95be720e232a8ff1a280151c49635d Package: CNVRanger Version: 1.25.4 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 MD5sum: 97b8f460b8422a80b946d23752796dc4 Package: CNVrd2 Version: 1.47.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: dbcba74d2a0520e4f17780915a453204 Package: CoCiteStats Version: 1.81.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 0c135b649fefca0ed7a1e360ed489db0 Package: COCOA Version: 2.23.1 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 0020e79dddeffbef4f45996a7174d372 Package: codelink Version: 1.77.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: 3ea538298dff4514802909b14ecf088f Package: CODEX Version: 1.41.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 3b259ae4cdfba86bac6fd4c527122ee8 Package: CoGAPS Version: 3.29.1 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH, testthat Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache, xml2 License: BSD_3_clause + file LICENSE MD5sum: ec1e1a241c050338edf44daf13f3a166 Package: cogena Version: 1.43.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 1c181e26c2b487922f1b6514c45d3163 Package: cogeqc Version: 1.13.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: 7bed2d510638398dea46c374355794f1 Package: Cogito Version: 1.15.2 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, Seqinfo, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 66db6150c1ec7b54740cd3efa085ba92 Package: coGPS Version: 1.53.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: c7ce186aa91a4fc1fce5722f0f61d825 Package: cola Version: 2.15.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats (>= 1.2.0), GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 9babe6de8cee7f5ae7db5ba7c8b22f2c Package: combi Version: 1.21.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 97c858374b93fc1a11e0c01882ed9ac9 Package: coMethDMR Version: 1.13.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: b89f9c6ef9c36562082fd46fad6b301b Package: COMPASS Version: 1.47.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: efb85910bca9dccc51ce4baee7c766bf Package: compcodeR Version: 1.45.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: eba643f3fed684d6af5ff68109ded349 Package: compEpiTools Version: 1.43.1 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, Seqinfo Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 69371f141bfebf24816d04ac9ec7cfe5 Package: ComplexHeatmap Version: 2.25.2 Depends: R (>= 4.0.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: 8e2426a985aa147623f779151c8dd3da Package: CompoundDb Version: 1.13.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel, stringi Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: fcdbd5dc175f595bd8eb78302c88bf91 Package: ComPrAn Version: 1.17.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1d95724421e0fb01f9304df73d942e81 Package: compSPOT Version: 1.7.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 95b021aaa59aa80b9dbafeb7aa2810dd Package: concordexR 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BiocParallel, withr Suggests: knitr, rmarkdown, bluster, ComplexHeatmap, circlize, scater, viridis, scRNAseq, SingleR, MouseGastrulationData, testthat (>= 3.0.0), BiocStyle, scrapper License: GPL-3 MD5sum: 8449bc7e63911847fb87a28c59360022 Package: coRdon Version: 1.27.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 539863b94cc6b2e982d6f99d3327e5db Package: CoreGx Version: 2.13.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: d76748ae3d8fa09d8115eb5182fe6b8a Package: Cormotif Version: 1.55.0 Depends: R (>= 2.12.0), affy, 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SummarizedExperiment, grDevices, reshape2 , survival , survminer , ggplot2 , MTLR , glmnet , rms , preprocessCore , Matrix , stats, Hmisc, ggfortify, randomForestSRC, caret, SurvMetrics, MASS, Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 | file LICENSE MD5sum: bcba868a5798e6cdb9db792a2e2df221 Package: cpvSNP Version: 1.41.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 969e8e524828ea9c18b5a4bd296af00b Package: cqn Version: 1.55.0 Depends: R (>= 2.10.0), mclust Imports: splines, graphics, nor1mix, stats, quantreg Suggests: scales, edgeR License: Artistic-2.0 MD5sum: 34586be62b624d1363d83013c7198f5c Package: CRImage Version: 1.57.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: e61c0444da3ccb5920234cd105efe6bc 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crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings (>= 2.77.2), BSgenome (>= 1.77.1), crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb (>= 1.45.7), GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), IRanges, Matrix, MatrixGenerics, methods, rtracklayer (>= 1.69.1), S4Vectors, Seqinfo, stats, txdbmaker (>= 1.5.6), utils, VariantAnnotation (>= 1.55.1) Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: 6e714e0a9e10bd3b7e8b51c8ceeb6976 Package: crisprScore Version: 1.13.1 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a14e915caa4f2751f67a511675751721 Package: CRISPRseek Version: 1.49.1 Depends: R (>= 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MIT + file LICENSE MD5sum: c0b0d639f07a5f4996d6573d2a4ced2b Package: CrispRVariants Version: 1.37.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: b7a80c68b7787289ef7962187977480b Package: crisprVerse Version: 1.11.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE MD5sum: 59a3491e6006c8f9b93266c1cac6d70a Package: crisprViz Version: 1.11.1 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, Seqinfo, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: 98a454ab296a1ba7db015bb4d39d3285 Package: crlmm Version: 1.67.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit License: Artistic-2.0 MD5sum: ef9fca40641af263c8a404b768f5aefe Package: crumblr Version: 1.1.0 Depends: R (>= 4.4.0), ggplot2, methods Imports: Rdpack, viridis, tidytree, variancePartition (>= 1.36.3), SingleCellExperiment, ggtree, dplyr, stats, MASS, Rfast Suggests: BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat, ExperimentHub, scater, HMP, reshape2, glue, tidyverse, BiocGenerics, compositions License: Artistic-2.0 MD5sum: e6e6d9468410d92904a54ba1f5f9c22f Package: crupR Version: 1.1.1 Depends: R (>= 4.4.0) Imports: bamsignals, Rsamtools, GenomicRanges, preprocessCore, randomForest, rtracklayer, Seqinfo, S4Vectors, ggplot2, matrixStats, dplyr, IRanges, GenomicAlignments, GenomicFeatures, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, reshape2, magrittr, stats, utils, grDevices, SummarizedExperiment, BiocParallel, fs, methods Suggests: GenomeInfoDb, testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: c2de33bc081135b1f258688abf67b146 Package: CSAR Version: 1.61.1 Depends: R (>= 2.15.0), S4Vectors, IRanges, Seqinfo, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 4d9270fd2e4df86fd61e06f4ca5ac993 Package: csaw Version: 1.43.1 Depends: R (>= 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wesanderson Suggests: BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle, stringr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7fd5e42c8afcb52d66da38d7e4364f07 Package: CSSQ Version: 1.21.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, markdown License: Artistic-2.0 MD5sum: d11256f3f03ba967bd855a68a3fe248b Package: ctc Version: 1.83.0 Depends: amap License: GPL-2 MD5sum: ab77576c29a5943a461d196a7768e79d Package: CTdata Version: 1.9.0 Depends: R (>= 4.2) Imports: ExperimentHub, utils Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: 76d603292198789830e790677d6c0a5d Package: CTDquerier Version: 2.17.0 Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d4e943cb0fb3598cabd91897589cc996 Package: CTexploreR Version: 1.5.0 Depends: R (>= 4.3), CTdata (>= 1.5.3) Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap License: Artistic-2.0 MD5sum: b7284814181f02856a5cca0e4d2796c4 Package: cTRAP Version: 1.27.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: e53031a391b3ab358f921dac1de98cb9 Package: ctsGE Version: 1.35.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: f54dc9c107c89a32501de0fa64599788 Package: CTSV Version: 1.11.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: 313cda76f9f7fdf540060644c83f54db Package: CuratedAtlasQueryR Version: 1.7.0 Depends: R (>= 4.2.0) Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot License: GPL-3 MD5sum: 2af26a004352f13a44172029da85118d Package: customCMPdb Version: 1.19.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: f81e437ac947a03d788bb1a827a5bcc5 Package: cyanoFilter Version: 1.17.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: 0f7168fd63af7e8a3dd388be8abf16e9 Package: cycle Version: 1.63.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: e02648aac88f99d202978f4c53f58e2f Package: cydar Version: 1.33.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: 16e1a8302958339a4753d6493a2a0ab9 Package: cypress Version: 1.5.0 Depends: R(>= 4.4.0) Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 MD5sum: e8a97030d38bb2a2934a09f194ecbf2a Package: CytoDx Version: 1.29.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 4fbe38cc6340596c43180837a57bea77 Package: CyTOFpower Version: 1.15.0 Depends: R (>= 4.1) Imports: CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods, rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix, SummarizedExperiment, tibble, tidyr Suggests: testthat (>= 3.0.0), BiocStyle, knitr License: LGPL-3 MD5sum: 698b6b7618c24cd82fe83053e721d9ee Package: CytoGLMM Version: 1.17.3 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 8f711b617b279f9ba2fc16cc31b40429 Package: cytoKernel Version: 1.15.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 2b304bc804754bac27e991912bbcfeea Package: cytolib Version: 2.21.0 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no MD5sum: 9d514597cd2eb751dec7de0ebcaf79e4 Package: cytomapper Version: 1.21.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 3e48d3e582bdd002bd5c1363623e8d1b Package: CytoMDS Version: 1.5.0 Depends: R (>= 4.4), Biobase Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: fcfdd81189342bf3dffdfeafa270fd5d Package: cytoMEM 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knitr, rmarkdown, BiocStyle, reshape2, dplyr, CytoPipelineGUI License: GPL-3 MD5sum: eba1bba46916bd0edaad0ca8ba543102 Package: CytoPipelineGUI Version: 1.7.2 Depends: R (>= 4.4), CytoPipeline (>= 1.9.3) Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: ed07a9a07795a9fd924dfaede631df8b Package: cytoviewer Version: 1.9.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: fddbb0e072b8d9b082f8853cc8816faa Package: dada2 Version: 1.37.0 Depends: R (>= 4.1.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges 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graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: cf8ed97b01e62809dcef21aef4157a83 Package: DCATS Version: 1.7.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 30c12a3a9de0072328bfc2115202ea62 Package: dcGSA Version: 1.37.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 0692156be85c34d12e9de1727a595d24 Package: ddCt Version: 1.65.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: cf45e545022ea93bc08a86ca9feb1dea Package: ddPCRclust Version: 1.29.0 Depends: R (>= 3.5) 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org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE MD5sum: d84a50c75126b313ad92381ff64c2e17 Package: DECIPHER Version: 3.5.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: 3d403f3a72ce3e69e2ab083cdad03170 Package: decontam Version: 1.29.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: e3a290ea0126dc78a6a99f86bffe06f3 Package: decontX Version: 1.7.0 Depends: R (>= 4.3.0) Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ebf7160ee32f6ebfcea369cfca7d3974 Package: DeconvoBuddies Version: 1.1.5 Depends: R (>= 4.4.0) Imports: AnnotationHub, BiocFileCache, DelayedMatrixStats, dplyr, ExperimentHub, ggplot2, graphics, grDevices, MatrixGenerics, methods, purrr, rafalib, reshape2, S4Vectors, scran, SingleCellExperiment, spatialLIBD, stats, stringr, SummarizedExperiment, tibble, utils Suggests: Biobase, BiocStyle, covr, HDF5Array, knitr, RColorBrewer, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr, tidyverse License: Artistic-2.0 MD5sum: ee0264f9b0c40d1e44fffc41e5d4976a Package: deconvR Version: 1.15.1 Depends: R (>= 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file LICENSE MD5sum: a6eba7d351cd3559080c6ae95c5ab83b Package: DeepPINCS Version: 1.17.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 506e06d4293f14866d5fe91ba62bcf8e Package: deepSNV Version: 1.55.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 7495e27baeeabdeff264ca170ebbed82 Package: DeepTarget Version: 1.3.0 Depends: R (>= 4.2.0) Imports: fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: dd0f4752a9f1f067746be23d7f3990de Package: DEFormats Version: 1.37.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: bacf5bf8106569acd28bf5caf2aa0586 Package: DegCre Version: 1.5.1 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, Seqinfo, IRanges, BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: bc7264172c5c2820376f558ce5066007 Package: DegNorm Version: 1.19.1 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: 9a7a8bc2c02dd8d74c3ca5770aa6a653 Package: DEGseq Version: 1.63.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 8218a35350513bd26a0d04a993f80ea5 Package: DelayedArray Version: 0.35.3 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3), S4Arrays (>= 1.5.4), SparseArray (>= 1.7.5) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: b96e78543fc0cd4ad42ce62faab81e3b Package: DelayedDataFrame Version: 1.25.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 MD5sum: cbff0c7f6108e9368a05a9d1fa7b9459 Package: DelayedMatrixStats Version: 1.31.0 Depends: MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7) Imports: methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>= 1.5.19) Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) License: MIT + file LICENSE MD5sum: 9daf6bba2b0d968b029f95ad2d143bcb Package: DelayedRandomArray Version: 1.17.0 Depends: SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6) Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: 34d12e0eb508e240f37c7202eb8798fb Package: DelayedTensor Version: 1.15.0 Depends: R (>= 4.1.0) Imports: methods, utils, S4Arrays, SparseArray, DelayedArray (>= 0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray (>= 1.13.1), irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 MD5sum: 2b606927dff8143b54b75dc07f93c2b7 Package: deltaCaptureC Version: 1.23.1 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 618a48f2a80a9646bcbd685fb1209d3c Package: deltaGseg Version: 1.49.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: 1ff9b8dcebca0e2247fb84386149b2fe Package: DeMAND Version: 1.39.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: f09187398a644a5d16852a3e07e1c1e6 Package: DeMixT Version: 1.25.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend, psych, sva Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 MD5sum: 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assertthat, gridExtra, grid, stats, imputeLCMD, cluster Suggests: testthat, enrichR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 2b58714b7c279eec051edefc7a5a6632 Package: DepecheR Version: 1.25.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1), collapse (>= 1.9.2), ClusterR (>= 1.3.2) LinkingTo: Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 62cfa27ec0e6db6b60f2b38cbc4489e0 Package: DepInfeR Version: 1.13.0 Depends: R (>= 4.2.0) Imports: matrixStats, glmnet, stats, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm License: GPL-3 MD5sum: ce4c2144ac9cf7f0a1672553b263e2d0 Package: DEqMS Version: 1.27.1 Depends: R(>= 3.5),graphics,stats,ggplot2,matrixStats,dplyr,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 5256e89b4806c03382d1256f27816445 Package: derfinder Version: 1.43.1 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.9), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.61.1), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 2.25.1), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: bb9fc55005ce9d8ff420190e6e816aeb Package: derfinderHelper Version: 1.43.0 Depends: R(>= 3.2.2) Imports: IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2) Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr License: Artistic-2.0 MD5sum: c7401211244701a64adb89003ffaba70 Package: derfinderPlot Version: 1.43.1 Depends: R(>= 3.2) Imports: derfinder (>= 1.1.0), Seqinfo, GenomeInfoDb (>= 1.45.9), GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, 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SummarizedExperiment, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.39.6), AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18) Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter Suggests: GenomeInfoDb, GenomicFeatures, txdbmaker, pasilla (>= 0.2.22), BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi License: GPL (>= 3) MD5sum: b9d695b71e1e62e1722fc9dee20c2704 Package: DFP Version: 1.67.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 MD5sum: c08efb91f348a938ef3de0648a58fbc2 Package: DFplyr Version: 1.3.2 Depends: R (>= 4.1.0), dplyr Imports: BiocGenerics, methods, rlang, S4Vectors, tidyselect Suggests: BiocStyle, GenomeInfoDb, GenomicRanges, IRanges, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), tibble License: GPL-3 MD5sum: 58f3a44bf5d185f3d19275218ea1d752 Package: DiffBind Version: 3.19.0 Depends: R (>= 4.0), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP LinkingTo: Rhtslib (>= 1.99.1), Rcpp Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid License: Artistic-2.0 MD5sum: d8b42154381b67e17ed9fc030ea5beaf Package: diffcoexp Version: 1.29.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery, RUnit License: GPL (> 2) MD5sum: b47f7e07e5bb8f1acc8238a62817949c Package: diffcyt Version: 1.29.0 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: 022cba6de3b919929231338c87f9d4a7 Package: DifferentialRegulation Version: 2.7.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport, gridExtra LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 819ed61c5609df32f0eee0b91688552c Package: diffGeneAnalysis Version: 1.91.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: 75bc75227eba53477dfaea11b6f2929e Package: diffHic Version: 1.41.0 Depends: R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer LinkingTo: Rhtslib (>= 1.13.1), Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat License: GPL-3 MD5sum: 995d8e2de9a91f8eab7841545f7f6ac6 Package: DiffLogo Version: 2.33.0 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) MD5sum: 0de520452c91929fab93d0edf9b9b600 Package: diffuStats Version: 1.29.0 Depends: R (>= 3.4) Imports: grDevices, stats, methods, Matrix, MASS, checkmate, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils License: GPL-3 MD5sum: 7ad8dce6a947b20223e543b35f0f9fe2 Package: diffUTR Version: 1.17.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq, GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, ensembldb, viridisLite Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 6096b23c08bfe9394e2aa2799234de9f Package: diggit Version: 1.41.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE MD5sum: 4da4762edaf3138da514bc17db2aeda9 Package: Dino Version: 1.15.0 Depends: R (>= 4.0.0) Imports: BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin License: GPL-3 MD5sum: 1661d359107d4c277d83ac30dc8b3d65 Package: dinoR Version: 1.5.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR, GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr, tibble, tidyr, tidyselect Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 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heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: 4a74ee7bdc538784c69967c5c2de2815 Package: distinct Version: 1.21.0 Depends: R (>= 4.3) Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle License: GPL (>= 3) MD5sum: a2cb7a427d789236e00c48feb2be3473 Package: dittoSeq Version: 1.21.1 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran, MASS License: MIT + file LICENSE MD5sum: 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Package: DMRcaller Version: 1.41.2 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils, Rsamtools, GenomicRanges, GenomicAlignments, Biostrings, BSgenome, BiocManager, S4Vectors, IRanges, InteractionSet, stringr, inflection, BiocParallel, Seqinfo, GenomeInfoDb Suggests: knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 MD5sum: 43071e2a6794616d4cc6d8b75638c55e Package: DMRcate Version: 3.5.2 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, Seqinfo, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, GenomeInfoDb, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, 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stats, stringr, utils, SummarizedExperiment Suggests: BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap, rmarkdown, testthat (>= 3.0.0), withr, airway Enhances: massdataset License: MIT + file LICENSE MD5sum: 10010a2462045e11c6b2c7338315aece Package: DominoEffect Version: 1.29.5 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, Seqinfo, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 0d4c7b822bcdb4da2c0412fe1f2ddedc Package: dominoSignal Version: 1.3.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr, dplyr Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: ece3c9980b50d53b5492dade2e353f8a Package: doppelgangR Version: 1.37.3 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: ea86cb967add31d3a6441c726eee1f50 Package: Doscheda Version: 1.31.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 859e1a7e70b22ee70fa4dbac8d9d0854 Package: DOSE Version: 4.3.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils (>= 0.1.6) Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 MD5sum: 23b3376b49aedc83559df3bc7e4615c0 Package: doseR Version: 1.25.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 7715ec9a93aa0244f68bd26acb930692 Package: doubletrouble Version: 1.9.1 Depends: R (>= 4.2.0) Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 9499d53bbe03ba3fd187acc606c36728 Package: dreamlet Version: 1.7.1 Depends: R (>= 4.3.0), variancePartition (>= 1.36.1), SingleCellExperiment, ggplot2 Imports: edgeR, SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, 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DESeq2, rmarkdown License: Artistic-2.0 MD5sum: 5a533a49279592abb0a570b0d50584c0 Package: edge Version: 2.41.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE MD5sum: c79944fe067255836be6ded7cae54196 Package: edgeR Version: 4.7.6 Depends: R (>= 3.6.0), limma (>= 3.63.6) Imports: methods, graphics, stats, utils, locfit Suggests: arrow, jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db, SummarizedExperiment License: GPL (>= 2) MD5sum: 12885d771c6b90c3bff80ea20da64274 Package: EDIRquery Version: 1.9.0 Depends: R (>= 4.2.0) Imports: tibble (>= 3.1.6), tictoc (>= 1.0.1), utils (>= 4.1.3), stats (>= 4.1.3), readr (>= 2.1.2), InteractionSet (>= 1.22.0), GenomicRanges (>= 1.46.1) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 87630d985b8632d05dd629d38b85aea6 Package: eds Version: 1.11.0 Depends: Matrix 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d843900f7a76718eb065568ad8161d13 Package: eiR Version: 1.49.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite,codetools License: Artistic-2.0 MD5sum: bc2d1412c90b1749f0afbed31326bc70 Package: eisaR Version: 1.21.1 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer, withr License: GPL-3 MD5sum: 092f38c96ee15e5eb2d02464bbe4cf09 Package: ELMER Version: 2.33.1 Depends: R (>= 3.4.0), ELMER.data (>= 2.9.3) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, Seqinfo, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer (>= 1.61.2), DelayedArray Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData License: GPL-3 MD5sum: 939836da3ee32698dcbe2ceca6bd491b Package: ELViS Version: 1.1.12 Depends: R (>= 4.5.0) Imports: reticulate, BiocGenerics, circlize, ComplexHeatmap, data.table, dplyr, GenomicFeatures, GenomicRanges, ggplot2, glue, graphics, grDevices, igraph, IRanges, magrittr, memoise, methods, parallel, patchwork, scales, segclust2d, stats, stringr, txdbmaker, utils, uuid, zoo Suggests: Rsamtools, BiocManager, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 315484261f1704f72fce0424b41e76d3 Package: EMDomics Version: 2.39.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: ef452b22c57f67173cc1c7eae8b8a6af Package: EmpiricalBrownsMethod Version: 1.37.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3b2816d7656262edb72fa736ecf577e5 Package: enhancerHomologSearch Version: 1.15.1 Depends: R (>= 4.1.0), methods Imports: BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, pwalign, rtracklayer, Rcpp, S4Vectors, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools License: GPL (>= 2) MD5sum: c76c96e91d54cb354d4bacc9e44a5bb6 Package: EnMCB Version: 1.21.0 Depends: R (>= 4.0) Imports: survivalROC, glmnet, rms, mboost, Matrix, igraph, methods, survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown License: GPL-2 MD5sum: d86b0559bcc1397ba74b2df393365d61 Package: ENmix Version: 1.45.3 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats,R (>= 3.5.0) Imports: grDevices,graphics,matrixStats,methods,utils,irlba, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 737f639942a2aa1d5bf91a7a8fce05d5 Package: EnrichDO Version: 1.3.1 Depends: R (>= 4.0.0) Imports: BiocGenerics, Rgraphviz, hash, S4Vectors, dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics, utils, purrr, tidyr, stats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 924a84aa5ea03ced0c76db2d4a56d911 Package: EnrichedHeatmap Version: 1.39.1 Depends: R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: 624993d7b3749035e785bfe536d36854 Package: EnrichmentBrowser Version: 2.39.2 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod License: Artistic-2.0 MD5sum: 70b0099a39a0cf37fe904f83a6e3f6bb Package: enrichplot Version: 1.29.2 Depends: R (>= 4.1.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7), ggnewscale, ggplot2 (>= 3.5.0), ggrepel (>= 0.9.0), ggtangle (>= 0.0.5), graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6) Suggests: clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: 54895c5802d5c497c0c271f54c3f2925 Package: enrichViewNet Version: 1.7.2 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick License: Artistic-2.0 MD5sum: bf93883415c4b5804b2c6154ad5565c7 Package: ensembldb Version: 2.33.2 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationDbi (>= 1.31.19), rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.77.2), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: 15bb27a1c20cc10bad471f86aae42b0f Package: epialleleR Version: 1.17.1 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: d990d55e825eb752f86af90deb42d4eb Package: EpiCompare Version: 1.13.2 Depends: R (>= 4.2.0) Imports: AnnotationHub, ChIPseeker, data.table, genomation, GenomicRanges, IRanges (>= 2.41.3), Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), ggplot2 (>= 3.5.0), htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics, downloadthis, parallel Suggests: rworkflows, BiocFileCache, BiocParallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis License: GPL-3 MD5sum: 01b56b5420ce1cc123ef7148b8801e25 Package: epidecodeR Version: 1.17.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: da75b348f6d421c6310324d755c86576 Package: EpiDISH Version: 2.25.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 47477a7f709094fd0affc3f474e5f882 Package: epigraHMM Version: 1.17.3 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, Seqinfo, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: 15da835398e49ebc11ba4aebd2c533c8 Package: EpiMix Version: 1.11.1 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: 854edb557b819ddbe311981ab30d557a Package: epimutacions Version: 1.13.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: fa7f96f87b3faa31f8a4115c30592155 Package: epiNEM Version: 1.33.0 Depends: R (>= 4.1) Imports: BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: 3f4516b2d1347494aabc872e850bf4ff Package: EpipwR Version: 1.3.1 Depends: R (>= 4.4.0) Imports: EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo License: Artistic-2.0 MD5sum: 96b94d1d56b0bdddadcd2e6502696c49 Package: epiregulon Version: 1.5.1 Depends: R (>= 4.4), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, bluster, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, scMultiome, GenomeInfoDb, GenomicRanges, AUCell, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat LinkingTo: Rcpp, beachmat, assorthead Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater, beachmat.hdf5 License: MIT + file LICENSE MD5sum: 5c3be775bd53e9ca28de0758455491a0 Package: epiregulon.extra Version: 1.5.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, patchwork, reshape2, scales, scater Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), msigdb, GSEABase, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: 9b07daa3d349937baca25e854d24dd4a Package: epistack Version: 1.15.1 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: 0b49c640f162209c4d578ad70a135040 Package: epistasisGA Version: 1.11.2 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: 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Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: a8a5219cac7403669b080a39edfe4818 Package: epivizrData Version: 1.37.2 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), OrganismDbi, GenomicFeatures (>= 1.61.4), Seqinfo, IRanges, ensembldb (>= 2.33.1) Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: b2e9905f29e7553be6b94dbc83066ee9 Package: 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ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), apeglm (>= 1.4.2), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: b07ae8f58abd2cb234b7f6d29d842f9a Package: esATAC Version: 1.31.1 Depends: R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicAlignments, GenomicFeatures, R.utils, Seqinfo, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc License: GPL-3 | file LICENSE Archs: x64 MD5sum: 354cb23ff466df2d8fc4d9e004e179da Package: escape Version: 2.5.5 Depends: R (>= 4.1) Imports: ggdist, ggplot2 (>= 3.5.0), grDevices, Matrix, MatrixGenerics, methods, stats, SummarizedExperiment, utils Suggests: AUCell, BiocParallel, BiocStyle, DelayedMatrixStats, dplyr, fgsea, GSEABase, ggraph, ggridges, ggpointdensity, GSVA, hexbin, igraph, irlba, knitr, msigdb, patchwork, rmarkdown, rlang, scran, SeuratObject, Seurat, SingleCellExperiment, spelling, stringr, testthat (>= 3.0.0), UCell License: MIT + file LICENSE MD5sum: 24a9a336e46e661827c799c86fc89771 Package: escheR Version: 1.9.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: 16fad1fc1e7961dc0d25d7920a580cb8 Package: esetVis Version: 1.35.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: 7a06af875e0a61e4bd08bb71d8629ec6 Package: eudysbiome Version: 1.39.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: a73bd73f4f03ac7f1d00a95bf833fcef Package: evaluomeR Version: 1.25.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: dc420ea21aaa1c15ebc436418cd1ce0d Package: EventPointer Version: 3.17.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: cc6b0aa8f2c82c8ac9465b0a85845be4 Package: ExCluster Version: 1.27.0 Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges Imports: stats, methods, grDevices, graphics, utils License: GPL-3 MD5sum: aa4718569b37bcac8d4c6e22454e319a Package: ExiMiR Version: 2.51.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) Suggests: mirna10cdf License: GPL-2 MD5sum: 5b97d41ba056721a1dc9fef038a7a4fe Package: ExperimentHub Version: 2.99.5 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.99.3), BiocFileCache (>= 2.99.3) Imports: utils, S4Vectors, BiocManager, rappdirs Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments Enhances: ExperimentHubData License: Artistic-2.0 MD5sum: 16b0666864f078ec7fdd099e3fe66c13 Package: ExperimentHubData Version: 1.35.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.21.3) Imports: methods, ExperimentHub, BiocManager, DBI, httr, curl Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 142cbf6b2f29b992f977bacf38ba073b Package: ExperimentSubset Version: 1.19.0 Depends: R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE MD5sum: 3f97c3e7957f786d83cc23eed1426a10 Package: ExploreModelMatrix Version: 1.21.2 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs, rlang Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE MD5sum: 6bdf2b3f585881874dfa9ec5f8854358 Package: ExpressionAtlas Version: 2.1.1 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 09e7cb84e8418c67a2450f26e1636d7b Package: extraChIPs Version: 1.13.3 Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 4.0.0), ggside (>= 0.4.0), Seqinfo, SummarizedExperiment (>= 1.39.1), tibble Imports: csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb, glue, ggrepel, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, vctrs Suggests: apeglm, BiocStyle, SimpleUpset, covr, DESeq2, EnrichedHeatmap, GenomicAlignments, GenomicInteractions, Gviz, ggforce, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse, VennDiagram License: GPL-3 MD5sum: 284e5bb29b4ff509605b20763f9374d6 Package: fabia Version: 2.55.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 068c21474de5eac22cde4b034c4cee63 Package: factDesign Version: 1.85.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL MD5sum: 92f0c536fc3ae413386bb8ae6058dbae Package: faers Version: 1.5.2 Depends: R (>= 3.5.0) Imports: BiocParallel, brio, cli, curl (>= 6.0.0), data.table, httr2 (>= 1.0.0), MCMCpack, methods, openEBGM, rlang, rvest, tools, utils, vroom, xml2 Suggests: BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 01adac8dfc2840903d6053bc907c87dd Package: FamAgg Version: 1.37.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), 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MIT + file LICENSE MD5sum: 9e0dfe8c493daed16669493f691d3acf Package: fenr Version: 1.7.1 Depends: R (>= 4.1.0) Imports: tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect, tibble, purrr, readr, stringr, httr2, rvest, progress, BiocFileCache, shiny, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO License: MIT + file LICENSE MD5sum: 6e17b563da133a8f1f7e08f980e3be70 Package: ffpe Version: 1.53.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: 9352506b8d401c47d70fa58374d90630 Package: fgga Version: 1.17.0 Depends: R (>= 4.3), RBGL Imports: graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl, igraph Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle License: GPL-3 MD5sum: 63fedd35b3b5f01989d77a594c7f13cd Package: FGNet Version: 3.43.0 Depends: R (>= 4.2.0) Imports: igraph (>= 0.6), hwriter, R.utils, XML, 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graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table License: GPL-2 MD5sum: 5fb96a714218a41c2898f435257cf4fb Package: FitHiC Version: 1.35.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 656772da4e9b2bcca3408d6477f7f410 Package: FLAMES Version: 2.3.5 Depends: R (>= 4.2.0) Imports: abind, basilisk, bambu, BiocParallel, Biostrings, BiocGenerics, crew, circlize, ComplexHeatmap, cowplot, cli, dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments, Seqinfo, ggplot2, ggbio, grid, gridExtra, igraph, jsonlite, magrittr, magick, Matrix, MatrixGenerics, readr, reticulate, Rsamtools, rtracklayer, RColorBrewer, R.utils, S4Arrays, ShortRead, SingleCellExperiment, SummarizedExperiment, SpatialExperiment, scater, scatterpie, S4Vectors, scuttle, stats, scran, stringr, tidyr, utils, withr, methods, tibble, tidyselect, IRanges LinkingTo: Rcpp, Rhtslib, testthat Suggests: BiocStyle, GEOquery, ggrastr, knitr, rmarkdown, uwot, testthat (>= 3.0.0), xml2 License: GPL (>= 3) MD5sum: e069e3a88462225c966adaad993feb6f Package: flowAI Version: 1.39.0 Depends: R (>= 4.3.0) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny, BiocStyle License: GPL (>= 2) MD5sum: 0781706d246d232c1dfb808839003eb3 Package: flowBeads Version: 1.47.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: 40352f2d9f005e0a263967341d979814 Package: flowBin Version: 1.45.0 Depends: methods, 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GeneExpressionSignature Version: 1.55.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 573e4cb4a191932945184d8f4739e903 Package: genefilter Version: 1.91.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: a4deb74802523acc3797786a3c97b724 Package: genefu Version: 2.41.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: f14022832de1c76de0f66152a48be328 Package: GeneMeta Version: 1.81.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: d75b56b9b8061191e4830c5a857b78a6 Package: GeneNetworkBuilder Version: 1.51.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: ec4b19faaa05d1e6305867aef6c2d10e Package: GeneOverlap Version: 1.45.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 09bed67aaf594e5bff690e3ee5adb363 Package: geneplast Version: 1.35.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 0532781ea1a2f5651f560d7b1b91824c Package: geneplotter Version: 1.87.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: 5c633ac20f0dcb9a2fab00468429b1f6 Package: geneRecommender Version: 1.81.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: c4c77a933e6caf8037778d34e3f10e27 Package: GeneRegionScan Version: 1.65.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 09c7b31088246366b60b83e84d16ca8b Package: geneRxCluster Version: 1.45.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 9823477584e723608169d643bdda6f42 Package: GeneSelectMMD Version: 2.53.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 688be88eb1f57778db265502337da07e Package: GENESIS Version: 2.39.3 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb License: GPL-3 MD5sum: 86dc3d5c49de94a23dfe1ac2c474ae11 Package: GeneStructureTools Version: 1.29.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 4b562cb816bddb7b7015f3093340ee01 Package: geNetClassifier Version: 1.49.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 06a62e14df80018d0c9ddfbe460328d8 Package: GeneticsPed Version: 1.71.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 06882c1c8125a495c3827a5a2a23059d Package: geneXtendeR Version: 1.35.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: d17f388273e14220708d4962cf8a4dad Package: GENIE3 Version: 1.31.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 078ac011da4e16fc80b42f99066489a8 Package: genomation Version: 1.41.1 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, Seqinfo, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: f23da2b64950c534d972cdcd100150bf Package: GenomAutomorphism Version: 1.11.2 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, Seqinfo, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: d9fd4d172f863ff77efdfeba95ba041b Package: GenomeInfoDb Version: 1.45.12 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.41.1), Seqinfo (>= 0.99.2) Imports: stats, utils, UCSC.utils Suggests: GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: fbec96082f658a7e58df128f1044afe4 Package: genomeIntervals Version: 1.65.1 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: Seqinfo, GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: f9b911d604bacec037078459e2e25baa Package: genomes Version: 3.39.0 Depends: readr, curl License: GPL-3 MD5sum: 5604bb31395d7e3fa94a817dda9b6be9 Package: GenomicAlignments Version: 1.45.4 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: 5eccb937118e4f75e6739692e10d20c4 Package: GenomicDataCommons Version: 1.33.1 Depends: R (>= 4.1.0) Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: 53729d07bdbb273d95935f1d328953e3 Package: GenomicDistributions Version: 1.17.1 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: ba74ab1286144f6c33ab884a43cd87c7 Package: GenomicFeatures Version: 1.61.6 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.17.29), IRanges (>= 2.37.1), Seqinfo (>= 0.99.2), GenomicRanges (>= 1.61.1), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings (>= 2.77.2), rtracklayer (>= 1.69.1) Suggests: GenomeInfoDb, txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: b587a90f9cb69f5b11dc6719253a24e8 Package: GenomicFiles Version: 1.45.2 Depends: BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics, methods, Rsamtools (>= 2.25.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 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InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, Seqinfo, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 8808d34d8fcb6048e15e4ad8b5eafde3 Package: GenomicOZone Version: 1.23.1 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, Seqinfo, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 0a780dbdd8c5ee48a3124e08005065d4 Package: GenomicPlot Version: 1.7.2 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, Seqinfo, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi, GenomeInfoDb License: GPL-2 MD5sum: 5717d0f81b0c1de64ef2be5299d22abd Package: GenomicRanges Version: 1.61.5 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.41.1), Seqinfo Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: dedccb3dcabe5727a4b1427a301bad01 Package: GenomicScores Version: 2.21.4 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: c65cc6a70a217faf35b9027346e2a1d3 Package: GenomicSuperSignature Version: 1.17.1 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 85abec91fadce09fc3241dcc892f41f3 Package: GenomicTuples Version: 1.43.1 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), Seqinfo, S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings, GenomeInfoDb License: Artistic-2.0 MD5sum: b24c5c53a2a14918bf9d29071196ebea Package: GenProSeq Version: 1.13.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: fb65a09788c2dcec50fb710955c93a78 Package: GeoDiff Version: 1.15.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 9207ce3114760e4a26cea9963f2b4822 Package: GEOfastq Version: 1.17.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8993db9537ee5de7eec90d6e9ee737ff Package: GEOmetadb Version: 1.71.0 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 723f1c9679f65dd19358dff9d7078dc9 Package: geomeTriD Version: 1.3.18 Depends: R (>= 4.4.0) Imports: aricode, BiocGenerics, Biostrings, clue, cluster, dbscan, future.apply, Seqinfo, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, progressr, RANN, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 5a4cd654c51198db9be23384ff59b682 Package: GeomxTools Version: 3.13.1 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: b38a6590ce44072136daef5e4d134cf6 Package: GEOquery Version: 2.77.6 Depends: R (>= 4.1.0), methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2 Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown, quarto, DropletUtils, SingleCellExperiment License: MIT + file LICENSE MD5sum: 4e58cc3e59e538658218e0cde1e46171 Package: GEOsubmission Version: 1.61.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: 5320fa4ebce7198a6de3772b8301c765 Package: GeoTcgaData Version: 2.9.0 Depends: R (>= 4.2.0) Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics License: Artistic-2.0 MD5sum: fdb4a2d1d8b1cfdc550068ddb3a2bde8 Package: gep2pep Version: 1.29.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 73ec4d4ae6b7f7db1cff63b24a467af4 Package: getDEE2 Version: 1.19.3 Depends: R (>= 4.4) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: de2e676b06469f9bf525bfee70700b1c Package: geva Version: 1.17.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 9868bb87412c1934175b94d3d90767a5 Package: GEWIST Version: 1.53.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: ffdef78e070104c21686f3f3bd03c779 Package: geyser Version: 1.1.0 Depends: R (>= 3.5.0) Imports: bslib (>= 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Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), BSgenome (>= 1.77.1), VariantAnnotation (>= 1.55.1), rtracklayer (>= 1.69.1), GenomicFeatures (>= 1.61.4), OrganismDbi, ensembldb (>= 2.33.1), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 5ae99c0fa16266a890f6b76c66c665c3 Package: ggcyto Version: 1.37.1 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: dffbe1f16c323d27ce68ca37ae774709 Package: ggkegg Version: 1.7.2 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, methods, utils, stats, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, AnnotationDbi, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6d2038475915f3d2bed4ab16e719f1ff Package: ggmanh Version: 1.13.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, paletteer, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats, tidyr, dplyr, pals, magrittr Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), GenomicRanges License: MIT + file LICENSE MD5sum: dae84c3e080b2ff7f1a7a1399b9e35de Package: ggmsa Version: 1.15.1 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat (>= 3.0.0), yulab.utils License: Artistic-2.0 MD5sum: 01bb90a71b613be4dd1dd73167541d74 Package: GGPA Version: 1.21.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 177516dd736bcc95f658af295a7ddcfc Package: ggsc Version: 1.7.1 Depends: R (>= 4.1.0) Imports: Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS License: Artistic-2.0 MD5sum: 5be8fb08a4a97d95d267dc2deab1eeab Package: ggseqalign Version: 1.3.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 2dcf4a231839e12bb1eeca35efc31823 Package: ggspavis Version: 1.15.9 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, OSTA.data, VisiumIO, arrow, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: 12f418c7135037f4c02151d6b769e324 Package: ggtree Version: 3.99.0 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli, ggiraph (>= 0.9.1) Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue, Biostrings License: Artistic-2.0 MD5sum: b22a758df2ab2d4e821c00a7f6bc0a22 Package: ggtreeDendro Version: 1.11.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: af345b15b0fb12977b3b6443acb761f7 Package: ggtreeExtra Version: 1.19.1 Imports: ggplot2 (>= 4.0.0), utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: e5485662ebeb12734d3ae14850c56571 Package: ggtreeSpace Version: 1.5.0 Depends: R (>= 4.1.0) Imports: interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools, rlang, tibble, tidyr, tidyselect, stats Suggests: knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 144903e724a873c36d1ad57e998e6f91 Package: GIGSEA Version: 1.27.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: a7337bca8689a623cbd8653e600df963 Package: ginmappeR Version: 1.5.0 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem, jsonlite, rvest Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE MD5sum: 1542f69b88e03428abbcb03f84409564 Package: GLAD Version: 2.73.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 71d490407ced378dda2caf4ce007a927 Package: GladiaTOX Version: 1.25.3 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 182cf825cec4a55349f015cfc50c4ee1 Package: Glimma Version: 2.19.2 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran, scRNAseq, License: GPL-3 MD5sum: 879b2a402d2624082db3980cff039f04 Package: glmGamPoi Version: 1.21.0 Depends: R (>= 4.1.0) Imports: Rcpp, beachmat, DelayedMatrixStats, matrixStats, MatrixGenerics, SparseArray (>= 1.5.21), S4Vectors, DelayedArray, HDF5Array, Matrix, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs LinkingTo: Rcpp, RcppArmadillo, beachmat, assorthead Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, dplyr License: GPL-3 MD5sum: dbbaa781e97cc4ad22e2b2beec9bf7ff Package: glmSparseNet Version: 1.27.0 Depends: R (>= 4.3.0) Imports: biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2, glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet, Matrix, MultiAssayExperiment, SummarizedExperiment, survminer, TCGAutils, utils Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr License: GPL-3 MD5sum: 55f5610a3b6647bfcc6ed4197dd880a2 Package: GlobalAncova Version: 4.27.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: f378b3faa1ce9bb32a5f04b31188c1bb Package: globalSeq Version: 1.37.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 9e5728b88c6d178d91b6e84d62114246 Package: GloScope Version: 1.99.1 Depends: R (>= 4.4.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang, RColorBrewer, pheatmap, vegan, cluster, boot, permute Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 MD5sum: bb3ff0729767a397629084fc7f3adc0d Package: GmicR Version: 1.23.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: 83678a2a7c6d8a25f4c7052bd734de69 Package: gmoviz Version: 1.21.1 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, Seqinfo, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager, GenomeInfoDb License: GPL-3 MD5sum: 755cd78bb7c01d3d0063a185586128fd Package: GMRP Version: 1.37.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: c551533cce86ad1eccdb05ac2e9b3b4a Package: GNET2 Version: 1.25.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: c3a38507cbbe16689c110e1382c68bab Package: GNOSIS Version: 1.7.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0db0538e88922e950a7ae4d7ed5ac036 Package: GOexpress Version: 1.43.1 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: 8a1202f0ddd2cfe525f2623329580bae Package: GOfuncR Version: 1.29.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 5bd9fdb566ad9101328b7694b35b77a0 Package: GOpro Version: 1.35.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 9a1d58cf57a5cb845623f5a330723148 Package: goProfiles Version: 1.71.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: 507cb23305dd386cdcada8bdba02be8a Package: GOSemSim Version: 2.35.2 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils, stats, utils, yulab.utils (>= 0.2.1) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 06036bff698b4f3b1dbd8cfdbc3a89f1 Package: goseq Version: 1.61.1 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db, BiocGenerics, methods, rtracklayer, GenomicFeatures, Seqinfo Suggests: edgeR, org.Hs.eg.db License: LGPL (>= 2) MD5sum: bfc1ddd823af3989dbd4aeb5e647dffd Package: goSorensen Version: 1.11.0 Depends: R (>= 4.4) Imports: clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db, ggplot2, ggrepel, DT, magick License: GPL-3 MD5sum: a4c89e3804dfb29165d7efcd41770c86 Package: goSTAG Version: 1.33.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 25948ef12748e3f9d5faa7dc775b5c94 Package: GOstats Version: 2.75.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 7ae13b47f87cbc2cdef16b47a185c3b1 Package: GOTHiC Version: 1.45.1 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, Seqinfo Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: 6b0bdf93c3bff514d6e85b41c45f9607 Package: goTools Version: 1.83.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 020e60450e2976d939f6a376933f4571 Package: GPA Version: 1.21.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: aa3609a57322fdf4ec0777f2a0a5b506 Package: gpls Version: 1.81.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 386c15e8f891495b4646ea429e1dc3d0 Package: GrafGen Version: 1.5.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 MD5sum: 1f66e07f7e9afbb5a21a9ac00b7d654b Package: GRaNIE Version: 1.13.0 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork (>= 1.2.0), reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>= 1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, 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GPL (>= 2) MD5sum: 6053a109cabef3777c31b78ff318adf1 Package: graph Version: 1.87.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: 2edc77c9bc67487dec14ecdbf81c1d36 Package: GraphAlignment Version: 1.73.0 License: file LICENSE License_restricts_use: yes MD5sum: 8eb0a3a992daf0c6c9809409435edc07 Package: GraphAT Version: 1.81.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 4c505f386435e6186981c9b000763c1f Package: graphite Version: 1.55.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 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knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, sva, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: f9c600bbb8454b8d024f0f84232ff54d Package: gtrellis Version: 1.41.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: d06c7a1002e35af8a8dbdf6b8411b094 Package: GUIDEseq Version: 1.39.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 4151a0a59b709d1a98b682117f2884b3 Package: Guitar Version: 2.25.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 60a839dea3cf39ea56eff29254a65abc Package: gVenn Version: 0.99.1 Depends: R (>= 4.5.0) Imports: ComplexHeatmap, eulerr, GenomicRanges, IRanges, lubridate, methods, stringr, writexl Suggests: testthat (>= 3.0.0), ggplot2, withr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 154388da6d2b91a6c904d190614f4ea8 Package: Gviz Version: 1.53.1 Depends: R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.61.1), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.69.1), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 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snpStats, VariantAnnotation, AnnotationHub, data.table, tibble Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: b9a04eb8444a61e907b7ac4761e5c1fd Package: GWASTools Version: 1.55.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 MD5sum: 31ee42e2555ff731806e9c64a44db806 Package: gwasurvivr Version: 1.27.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: 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BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, SingleCellExperiment, DelayedMatrixStats, genefilter, RSpectra, RUnit, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 2f91b7d6f51d9f9e7b1d75c88664963e Package: HDTD Version: 1.43.0 Depends: R (>= 4.1) Imports: stats, Rcpp (>= 1.0.1) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 6b93a64b64caec358e0b78c29201edfc Package: hdxmsqc Version: 1.5.0 Depends: R(>= 4.3), QFeatures, S4Vectors, Spectra Imports: dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices, stats, MsCoreUtils Suggests: RColorBrewer, pheatmap, MASS, patchwork, testthat License: file LICENSE MD5sum: e4cd2d5904713cf70907d3f2f810dea9 Package: heatmaps Version: 1.33.1 Depends: R (>= 3.5.0) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, Seqinfo 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rlang, rtracklayer, S4Vectors, stats, utils, strawr, tibble, stringr, tidyr, gridExtra, data.table, reshape, checkmate, purrr, withr Suggests: GenomeInfoDb, covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1) License: MIT + file LICENSE MD5sum: 74fc170fd64d9282ee6a2e9eeea74665 Package: HiCaptuRe Version: 0.99.15 Depends: R (>= 4.5.0) Imports: Biostrings, BSgenome, cli, data.table, dplyr, GenomeInfoDb, GenomicInteractions, GenomicRanges, InteractionSet, ggplot2, ggpubr, ggVennDiagram, gplots, igraph, IRanges, memoise, methods, S4Vectors, stringr, tibble, tidyr, UpSetR, utils Suggests: BSgenome.Hsapiens.NCBI.GRCh38, knitr, rmarkdown, DT, testthat, BiocStyle, kableExtra License: GPL-3 MD5sum: 6828dea98aedfc93e84d40ae89d7368c Package: HiCBricks Version: 1.27.1 Depends: R (>= 3.6), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, Seqinfo, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3ad5f83f16242a48699ffdaee0bd02e2 Package: HiCcompare Version: 1.31.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: 7bfd37c475839e92974defc7216dc1d0 Package: HiCDCPlus Version: 1.17.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: f7d7be32283b38278192f9b14f2ff21f Package: HiCDOC Version: 1.11.2 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, Seqinfo LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 MD5sum: 9ddcba896f5ac7fbab071113aa076273 Package: HiCExperiment Version: 1.9.2 Depends: R (>= 4.2) Imports: InteractionSet, strawr, Seqinfo, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 84b9e1a4dc63763cf6ca2273c54819da Package: HiContacts Version: 1.11.0 Depends: R (>= 4.2), HiCExperiment Imports: InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1fcb97e6ed2b943d790ce953093f00e9 Package: HiCool Version: 1.9.1 Depends: R (>= 4.2), HiCExperiment Imports: BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet, vroom, basilisk.utils, basilisk, reticulate, rmarkdown, rmdformats, plotly, dplyr, stringr, sessioninfo, utils Suggests: HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9f3d8945dc9a58d38a1a52993a62c6d3 Package: HiCParser Version: 1.1.1 Imports: data.table, InteractionSet, GenomicRanges, SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools, pbapply, BiocGenerics, Seqinfo LinkingTo: Rcpp Suggests: rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: LGPL MD5sum: 2bbd966d3d0e8cb3dc2432a1d7cf7021 Package: HiCPotts Version: 0.99.6 Depends: R (>= 4.5) Imports: Rcpp(>= 0.11.0), parallel, stats, Biostrings, GenomicRanges, rtracklayer, strawr, rhdf5, BSgenome,IRanges, S4Vectors, BSgenome.Dmelanogaster.UCSC.dm6 LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr (>= 1.30), rmarkdown (>= 2.10), ggplot2 (>= 3.5.0), reshape2 (>= 1.4.4), testthat (>= 3.0.0), BiocManager License: GPL-3 MD5sum: cf4eb82d004beaf32002a045803e1df5 Package: hicVennDiagram Version: 1.7.3 Depends: R (>= 4.3.0) Imports: Seqinfo, GenomicRanges, IRanges, InteractionSet, rtracklayer, ggplot2, ComplexUpset, reshape2, eulerr, S4Vectors, methods, utils, htmlwidgets, svglite Suggests: BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid, TxDb.Hsapiens.UCSC.hg38.knownGene License: GPL-3 MD5sum: 4e71aba18043c9cf3edd034725d30afb Package: hierGWAS Version: 1.39.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 MD5sum: 897cfcc007456219faf786959b1ba9b4 Package: hierinf Version: 1.27.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE MD5sum: bf40960f53b03d063c74b5570b57d76f Package: HilbertCurve Version: 2.3.0 Depends: R (>= 4.0.0), grid Imports: methods, utils, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr, Rcpp LinkingTo: Rcpp Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown License: MIT + file LICENSE MD5sum: d49bf605b6cf708c8b79c40224f20401 Package: HilbertVis Version: 1.67.2 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: c17d08c90dbf06e915bf4d9c7dfe3e90 Package: HiLDA Version: 1.23.0 Depends: R(>= 4.1), ggplot2 Imports: R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges, S4Vectors, XVector, Biostrings, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 2de34c499c7d2428189c5ec97c06cd92 Package: HIPPO Version: 1.21.0 Depends: R (>= 3.6.0) Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 67e86308c70f2103d9959a6405342bae Package: HIREewas Version: 1.27.0 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) MD5sum: 48224f75fcb27c3ed7e0a894ffb08e25 Package: HiTC Version: 1.53.1 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, Seqinfo Suggests: BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 MD5sum: 7ee2ad32e1eea6cf4f6e1963211f774d Package: hmdbQuery Version: 1.29.0 Depends: R (>= 3.5), XML Imports: S4Vectors, methods, utils Suggests: knitr, annotate, gwascat, testthat, rmarkdown License: Artistic-2.0 MD5sum: 0104d9d75d116943faacc6f30827ca71 Package: HMMcopy Version: 1.51.0 Depends: R (>= 2.10.0), data.table (>= 1.11.8) License: GPL-3 MD5sum: b84039e7f41a7341b287e168770acc15 Package: HoloFoodR Version: 1.3.1 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment Imports: dplyr, httr2, jsonlite, S4Vectors, stringi, stats, SummarizedExperiment, utils Suggests: BiocStyle, DT, ggh4x, ggsignif, knitr, MGnifyR, mia, miaViz, MOFA2, patchwork, reticulate, rmarkdown, scater, shadowtext, testthat, UpSetR License: Artistic-2.0 | file LICENSE MD5sum: 51277b1a14e6c4c52fe1f71b9cadcf56 Package: hoodscanR Version: 1.7.0 Depends: R (>= 4.3) Imports: knitr, rmarkdown, SpatialExperiment, SummarizedExperiment, circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid, methods, stats, RANN, Rcpp (>= 1.0.9) LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 + file LICENSE MD5sum: ac8cd07e6933407a8c36c4fe92c2561d Package: hopach Version: 2.69.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: ad78441429837b33111becc06b5cb855 Package: HPAanalyze Version: 1.27.2 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: c99d8e177085c356b906cfbb51ed06ac Package: hpar Version: 1.51.0 Depends: R (>= 3.5.0) Imports: utils, ExperimentHub Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT License: Artistic-2.0 MD5sum: 34e7c44ffef9772a480d667096d60743 Package: HTqPCR Version: 1.63.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 MD5sum: 545da4a2482ee5ee23ce80f12d15e10b Package: HTSFilter Version: 1.49.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 6d0c338e93336e6cf7f76c4c164c1fd6 Package: HuBMAPR Version: 1.3.1 Depends: R (>= 4.4.0) Imports: httr2, dplyr, tidyr, tibble, rjsoncons, rlang, utils, stringr, whisker, purrr Suggests: testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle, pryr License: Artistic-2.0 MD5sum: d56cf3a3c6f2f0d2c75e374c3f83da77 Package: HubPub Version: 1.17.1 Imports: available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager, utils Suggests: AnnotationHubData, ExperimentHubData, GenomeInfoDbData, testthat, knitr, rmarkdown, BiocStyle, License: Artistic-2.0 MD5sum: 0aaeaf1fd657215df805d90103767e2c Package: hummingbird Version: 1.19.0 Depends: R (>= 4.0) Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: e7dde7db4ecc2b96d970aea196059e1a Package: HVP Version: 0.99.5 Imports: Matrix, methods, stats Suggests: SingleCellExperiment, SummarizedExperiment, Seurat, SeuratObject, ggplot2, progress, testthat, splatter, scater, devtools, knitr, rmarkdown, BiocStyle, ExperimentHub License: MIT + file LICENSE MD5sum: 298d55015a71c52fc2933f1881bf8224 Package: HybridExpress Version: 1.5.0 Depends: R (>= 4.3.0) Imports: ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment, stats, methods, RColorBrewer, ComplexHeatmap, grDevices, BiocParallel Suggests: BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: d04550f6e37023b821464ec6490468a1 Package: 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stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 MD5sum: de63edb9b2b7aa2c841ab4213531bcf5 Package: Ibex Version: 0.99.31 Depends: R (>= 4.5.0) Imports: basilisk, immApex (>= 1.3.2), methods, Matrix, reticulate (>= 1.43.0), rlang, SeuratObject, scRepertoire, SingleCellExperiment, stats, SummarizedExperiment, tensorflow, tools Suggests: basilisk.utils, BiocStyle, bluster, dplyr, ggplot2, kableExtra, knitr, markdown, mumosa, patchwork, Peptides, rmarkdown, scater, spelling, testthat (>= 3.0.0), utils, viridis License: MIT + file LICENSE MD5sum: 60d9ee68e702407dd54be979c74bcdd8 Package: ibh Version: 1.57.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) MD5sum: 816e858a30598198a037b6fe61937901 Package: Icens Version: 1.81.0 Depends: survival Imports: graphics License: Artistic-2.0 MD5sum: 551028987cc04ce7f2c26577b13fc7a5 Package: icetea Version: 1.27.1 Depends: R (>= 4.0) Imports: stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: GenomeInfoDb, knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: 64bd5bea8182e8404686d0d87f5d55e9 Package: iCheck Version: 1.39.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: 668e817d4606ec3acd8ecd6c1e3dd1d3 Package: iChip Version: 1.63.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: db37a139df89a3a2de7701cb60550d42 Package: iClusterPlus Version: 1.45.0 Depends: R (>= 4.1.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 5e63351ee7b896dce38e31357eaa2509 Package: iCNV Version: 1.29.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: ae4bfd6ca44a8ca75d35a015f7c81b8b Package: iCOBRA Version: 1.37.1 Depends: R (>= 4.4.0) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, utils, rlang Suggests: knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: e3fb6192dde1dbd8cefde02c1df4976f Package: ideal Version: 2.3.0 Depends: topGO Imports: DESeq2, SummarizedExperiment, mosdef (>= 1.1.0), GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, graphics, base64enc, methods, utils, stats Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR License: MIT + file LICENSE MD5sum: 854fd5098f701f0458116c65cd949d14 Package: IdeoViz Version: 1.45.0 Depends: R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer, graphics, GenomeInfoDb License: GPL-2 MD5sum: 4eb01058d5a917a108d91f9dadd5fbef Package: idiogram Version: 1.85.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: 8fa0c0dd13eece452e29015014a60f9e Package: idpr Version: 1.19.0 Depends: R (>= 4.1.0) Imports: ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings (>= 2.56.0), methods (>= 4.0.0) Suggests: knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr License: LGPL (>= 3) MD5sum: db26af984989c084d3b7e3f725bcb06a Package: idr2d Version: 1.23.1 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.6), futile.logger (>= 1.4.3), 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IRanges, GenomeInfoDb Suggests: GenomicAlignments, parallel, testthat, knitr, rmarkdown, BiocStyle, ggplot2, dplyr, scales, ggseqlogo License: Artistic-2.0 MD5sum: 8b239ec582b4ddbd19f0a15861d98629 Package: iGC Version: 1.39.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: e1a8b9b003b15609f71ff1152336cd2c Package: IgGeneUsage Version: 1.23.0 Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment, tidyr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork License: MIT + file LICENSE MD5sum: c22a78a26a574b29c41e8ea9e2667d83 Package: igvR Version: 1.29.0 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1) Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo License: MIT + file LICENSE MD5sum: 90a3824231f62f3b548cb5455504c5d9 Package: igvShiny Version: 1.5.0 Depends: R (>= 3.5.0), GenomicRanges, methods, shiny Imports: BiocGenerics, checkmate, futile.logger, GenomeInfoDbData, htmlwidgets, httr, jsonlite, randomcoloR, utils Suggests: BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer, RUnit, shinytest2, VariantAnnotation License: MIT + file LICENSE MD5sum: 1cfb8c8b4ae4c0202bb487881cdfcf46 Package: IHW Version: 1.37.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: f731a64149d11477ddaa37a6c976f4f6 Package: illuminaio Version: 0.51.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: a78c362c8d504cb116c9905ea9244b51 Package: ILoReg Version: 1.19.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment, SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: c369c2e0c9c100e4761bfb25d9c0683c Package: imageTCGA Version: 1.1.0 Depends: R (>= 3.5.0), shiny Imports: DT, dplyr, bslib, bsicons, ggplot2, viridis, tidyr, leaflet, clipr, rlang Suggests: BiocManager, BiocStyle, knitr, curl, glue, rmarkdown, sessioninfo, testthat, tibble, GenomicDataCommons License: Artistic-2.0 MD5sum: 2d845631291be1ab5f8a4e2f3d0c6e1d Package: IMMAN Version: 1.29.0 Imports: STRINGdb, pwalign, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 78b443f95303ec3f7796b0c02c0f1766 Package: immApex Version: 1.3.7 Depends: R (>= 4.3.0) Imports: hash, httr, Matrix, matrixStats, methods, Rcpp, rvest, SingleCellExperiment, stats, stringr, utils LinkingTo: Rcpp Suggests: BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown, Peptides, randomForest, rmarkdown, scRepertoire, spelling, testthat, tidygraph, viridis License: MIT + file LICENSE MD5sum: c5eeec08a53b51b9dfc1fffc171bf8a0 Package: immunoClust Version: 1.41.2 Depends: R(>= 4.2), flowCore Imports: methods, stats, graphics, grid, lattice, grDevices Suggests: BiocStyle, utils, testthat License: Artistic-2.0 MD5sum: c84b86ef683eda3fe2bad15ee4b5b641 Package: immunogenViewer Version: 1.3.1 Depends: R (>= 4.0) Imports: ggplot2, httr, jsonlite, patchwork, UniProt.ws Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT License: Apache License (>= 2) MD5sum: 50d9f730c75e53e3b6657c46fb6845a0 Package: immunotation Version: 1.17.5 Depends: R (>= 4.1) Imports: stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT License: GPL-3 MD5sum: ce8bd1bfc7c7aed0f2a3527a3e742959 Package: IMPCdata Version: 1.45.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE MD5sum: 23c62b4d91658940206dbd1d6a925249 Package: impute Version: 1.83.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 21ff9b10209d4301d47154e632308558 Package: INDEED Version: 2.23.0 Depends: glasso (>= 1.8), R (>= 3.5) Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1), utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 MD5sum: 8c1e1ae537e97840019733af47ebe24a Package: infercnv Version: 1.25.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: c6ef67e31df8e8a6e25e990148155a6b Package: infinityFlow Version: 1.19.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: 4cda867bc8e3dfc3b62bb8bb6268744c Package: Informeasure Version: 1.19.0 Depends: R (>= 4.0) Imports: entropy Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 485815ed2782892f1b70b05f92fcad06 Package: InPAS Version: 2.17.1 Depends: R (>= 3.5) Imports: AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq, depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr,methods,parallelly, plyranges, preprocessCore, readr,reshape2, RSQLite, Seqinfo, stats, S4Vectors, utils Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 2) MD5sum: 224956d2deb71df420ed39a3d181b0c6 Package: INPower Version: 1.45.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 817b3e0968b42ee68ba94a01e46704d8 Package: INSPEcT Version: 1.39.1 Depends: R (>= 3.6), methods, Biobase, BiocParallel Imports: pROC, deSolve, rootSolve, KernSmooth, readxl, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, Seqinfo, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: e222d7144bd98afdb36277f74ab4e244 Package: INTACT Version: 1.9.0 Depends: R (>= 4.3.0) Imports: SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2 Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE MD5sum: 0e179370824c8bddb2ab714d4844e28c Package: InTAD Version: 1.29.1 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: fd71845efeed78a5052501c59991f6f5 Package: intansv Version: 1.49.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: MIT + file LICENSE MD5sum: 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GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE MD5sum: f29e0caa17839eb6a3f33e876a60edab Package: interactiveDisplay Version: 1.47.1 Depends: R (>= 3.5.0), methods, BiocGenerics, grid Imports: interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: d431b6182dbba2d772c2515579948ccd Package: interactiveDisplayBase Version: 1.47.1 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: 989f593abe20ce05a568f9b0bef1448a Package: InterCellar Version: 2.15.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE MD5sum: 9b9348ccb4af2091a803ed7a45082a6a Package: IntEREst Version: 1.33.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles Imports: seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMariaDB, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: d367dd747e4e7e76fe8176121e385379 Package: IntramiRExploreR Version: 1.31.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 23205dfad4a851aac4769024cb497cfc Package: IONiseR Version: 2.33.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 8e23f951e970243dcd77f31deafeb882 Package: ipdDb Version: 1.27.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 3e8169a304637f03cc699799be56b1d1 Package: IRanges Version: 2.43.5 Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.4) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 945235f7ade152969c873a1c9456cede Package: ISAnalytics Version: 1.19.3 Depends: R (>= 4.5) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, vegan, data.table, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, Rcapture License: CC BY 4.0 MD5sum: beec47ffaa29c1608074fb218a8d8b44 Package: iSEE Version: 2.21.1 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: df29618bedeaad1610dc1b0d278f0b49 Package: iSEEde Version: 1.7.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 213c5854b59fdafdafb5e191ea688377 Package: iSEEfier Version: 1.5.0 Depends: R (>= 4.1.0) Imports: iSEE, iSEEu, methods, ggplot2, igraph, rlang, stats, SummarizedExperiment, SingleCellExperiment, visNetwork, BiocBaseUtils Suggests: knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 466824f5cd2fb5ab0aaaf30a9e33317e Package: iSEEhex Version: 1.11.0 Depends: SummarizedExperiment, iSEE Imports: ggplot2, hexbin, methods, shiny Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater License: Artistic-2.0 MD5sum: d78606539fa9f192b0d298809701cf3a Package: iSEEhub Version: 1.11.0 Depends: SummarizedExperiment, SingleCellExperiment, ExperimentHub Imports: AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs, S4Vectors, shiny, shinydashboard, shinyjs, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: 381cef46fd32862ed067ad289747dd76 Package: iSEEindex Version: 1.7.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs, shiny, shinydashboard, shinyjs, stringr, urltools, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, markdown, scRNAseq, sessioninfo, testthat (>= 3.0.0), yaml License: Artistic-2.0 MD5sum: 961a3de93ede9f03c1b8a4e5c8c91564 Package: iSEEpathways Version: 1.7.0 Depends: iSEE Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5a99d7d273d52a98e8956e4bf26feee1 Package: iSEEu Version: 1.21.0 Depends: iSEE, iSEEhex Imports: methods, S4Vectors, IRanges, shiny, SummarizedExperiment, SingleCellExperiment, ggplot2 (>= 3.4.0), DT, stats, colourpicker, shinyAce Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr License: MIT + file LICENSE MD5sum: 8719fb6e558e47a70b84c271eca4b4e3 Package: iSeq Version: 1.61.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 8fb4ad567f68e274af2b46f54ef82347 Package: ISLET Version: 1.11.0 Depends: R(>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls Imports: stats, methods, purrr, abind Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr License: GPL-2 MD5sum: 2233e9329cabee9b64f7460328127641 Package: islify Version: 1.1.1 Depends: R (>= 4.5) Imports: autothresholdr (>= 1.4.2), Matrix (>= 1.6.1), RBioFormats (>= 1.0.0), tiff (>= 0.1.12), png (>= 0.1.8), dbscan (>= 1.1.12), abind (>= 1.4.8), methods (>= 4.3.3), stats (>= 4.3.3) Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: f8172cf5f21cddfa2b082f03943d8259 Package: isobar Version: 1.55.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: 9ebf601708c2363aa01ca1b1db6ac222 Package: IsoBayes Version: 1.7.1 Depends: R (>= 4.3.0) Imports: methods, Rcpp, data.table, glue, stats, doParallel, parallel, doRNG, foreach, iterators, ggplot2, HDInterval, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 5952567b3e7b9cb567e5e20ab59ceb16 Package: IsoCorrectoR Version: 1.27.0 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 2395a84d46fd0d767b9cef0f675bfdcb Package: IsoCorrectoRGUI Version: 1.25.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 722d11725886494999252350f85a6458 Package: IsoformSwitchAnalyzeR Version: 2.9.1 Depends: R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, Seqinfo, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment, tidyr, S4Vectors, BiocParallel, pwalign Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown License: GPL (>= 2) MD5sum: 4c7f5d208a6ce2c37ce81ef308b1b6ea Package: ISoLDE Version: 1.37.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) MD5sum: 38a306f9e913951128aae23c8f6da197 Package: ITALICS Version: 2.69.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: 444941a61ad6886e3f0bc9cf6575dd7e Package: iterativeBMA Version: 1.67.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 7d048249fd276b23b7a89ffc9241bb1c Package: iterativeBMAsurv Version: 1.67.0 Depends: BMA, leaps, 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parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) MD5sum: 797473be45d0c835e74f49b09c1c8f59 Package: jazzPanda Version: 1.1.1 Depends: R (>= 4.5.0) Imports: spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr, doParallel, BiocParallel, methods, BumpyMatrix,SpatialExperiment Suggests: BiocStyle, knitr, rmarkdown, spatstat, Seurat, statmod, corrplot, ggplot2, ggraph, ggrepel, gridExtra, reshape2, igraph, jsonlite, vdiffr, patchwork, ggpubr, tidyr, SpatialFeatureExperiment, ExperimentHub, TENxXeniumData, SingleCellExperiment, SFEData, Matrix, data.table, scran, scater, grid, testthat (>= 3.0.0) License: GPL-3 MD5sum: e29f82a9687a6e28354235fc1f25edd8 Package: karyoploteR Version: 1.35.3 Depends: R (>= 3.4), regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, Seqinfo, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, 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limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0), gridExtra Suggests: knitr License: GPL (>= 2) MD5sum: bd1aca785d98354ce0867276afb37256 Package: knowYourCG Version: 1.5.2 Depends: R (>= 4.4.0) Imports: sesameData, dplyr, methods, rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel, tibble, wheatmap, magrittr Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2, ggrastr License: MIT + file LICENSE MD5sum: a8792951889853c54b1030b0608b79c7 Package: koinar Version: 1.3.0 Depends: R (>= 4.3) Imports: httr, jsonlite, methods, utils Suggests: BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice, msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat, mzR License: Apache License 2.0 MD5sum: 428b5fac86f96bf24817918883eec7d7 Package: LACE Version: 2.13.1 Depends: R (>= 4.2.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, 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License: GPL-3 MD5sum: b166c38546208b76cf57c901d5cfc139 Package: levi Version: 1.27.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods, rmarkdown LinkingTo: Rcpp Suggests: rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: da55a8e6be654bed46a4663da0dce17d Package: lfa Version: 2.9.0 Depends: R (>= 4.0) Imports: utils, methods, corpcor, RSpectra Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: da7dad68d6364db0a17a1d1d7273df1f Package: Lheuristic Version: 1.1.0 Depends: R (>= 4.4.0) Imports: Hmisc, stats, energy, grDevices, graphics, utils, MultiAssayExperiment, ggplot2, ggpubr Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: de7eb9d237a734a3cf18509353e2008d Package: limma Version: 3.65.5 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods, statmod Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn License: GPL (>= 2) MD5sum: f858b3b164e9338eccdaeaad1c593c5a Package: limmaGUI Version: 1.85.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: e7cb7afcb06fd661fbab4ac4cb2a482d Package: limpa Version: 1.1.6 Depends: limma Imports: methods, stats, data.table, statmod Suggests: arrow, knitr, BiocStyle License: GPL (>= 2) MD5sum: d15a8ec9e982856ccfbc82d9cdcdf818 Package: limpca Version: 1.5.1 Depends: R (>= 3.5.0) Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) 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lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: 96c47d82b640b71e17a37b7a361bb518 Package: LymphoSeq Version: 1.37.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: 7bb0b28da5d8c6640899edf2d45f47ef Package: M3C Version: 1.31.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: 4f5bb6a999bd120947141b7c5986b74b Package: M3Drop Version: 1.35.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase License: GPL (>= 2) MD5sum: 4408ca5d424bbb77c24737a96554c6cc Package: m6Aboost Version: 1.15.1 Depends: S4Vectors, adabag, GenomicRanges, R (>= 4.1) Imports: dplyr, rtracklayer, BSgenome, Biostrings, utils, methods, IRanges, ExperimentHub Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 62ffc8a47b74b1ff1772a1391cd511b9 Package: maCorrPlot Version: 1.79.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: 60966923040c2e7d7336f6d1cecbabc2 Package: MACSQuantifyR Version: 1.23.0 Imports: readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel, methods, stats, latticeExtra, lattice, rmarkdown, png, grid, gridExtra, prettydoc, rvest, xml2 Suggests: knitr, testthat, R.utils, spelling License: Artistic-2.0 MD5sum: bccb7bb09fb303f1aea2922085396f61 Package: MACSr Version: 1.17.0 Depends: R (>= 4.1.0) Imports: utils, reticulate, S4Vectors, methods, basilisk, ExperimentHub, AnnotationHub Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata License: BSD_3_clause + file LICENSE MD5sum: f7676ad15ae062ff2f97f1d21164529f Package: made4 Version: 1.83.0 Depends: RColorBrewer,gplots,scatterplot3d, Biobase, SummarizedExperiment Imports: ade4 Suggests: affy, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3f62dbfeed21ea0e9ee331ce38f42143 Package: maftools Version: 2.25.10 Depends: R (>= 4.1.0) Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy, pheatmap LinkingTo: Rhtslib Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors License: MIT + file LICENSE MD5sum: 1678655513a90c69106d285afd77b139 Package: MAGAR Version: 1.17.0 Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table, UpSetR, reshape2, jsonlite, methods, ff, argparse, impute, RnBeads.hg19, RnBeads.hg38, utils, stats Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager License: GPL-3 MD5sum: 7659299827f1f234006aa40bc5177e18 Package: magpie Version: 1.9.0 Depends: R (>= 4.3.0) Imports: utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle License: MIT + file LICENSE MD5sum: 1efc473a81b50431045b50d5446a5b99 Package: magrene Version: 1.11.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: 613ec5317db94f8dde57136cd4d0b828 Package: MAI Version: 1.15.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: bd547696802232829a5008c442666381 Package: makecdfenv Version: 1.85.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils License: GPL (>= 2) MD5sum: 89a14b9225bc9879f78aeacdcfac987a Package: MANOR Version: 1.81.0 Depends: R (>= 2.10) Imports: GLAD, graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, bookdown License: GPL-2 MD5sum: 4cdbcf009cf146add4b88a8a1e041bde Package: MantelCorr Version: 1.79.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: 29546dcd4a69b2832d619540cd15810f Package: MAPFX Version: 1.5.0 Depends: R (>= 4.4.0) Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2, RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils, e1071, xgboost, parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 9de008fa11a57da9c2a1463b6903b13f Package: maPredictDSC Version: 1.47.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: c56099e98c7825d2bfdab392d0558f65 Package: mapscape Version: 1.33.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: b7be6c63f8a3a2bbda25ab859d5eba38 Package: mariner Version: 1.9.1 Depends: R (>= 4.2.0) Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData, TxDb.Hsapiens.UCSC.hg38.knownGene, fields License: MIT + file LICENSE MD5sum: 3258cee99b91265cf552d83c40893315 Package: markeR Version: 0.99.6 Depends: R (>= 4.5.0) Imports: circlize, edgeR, ComplexHeatmap, ggh4x, ggplot2, ggpubr, grid, gridExtra, pROC, RColorBrewer, reshape2, rstatix, scales, stats, utils, fgsea, limma, ggrepel, effectsize, msigdbr, tibble Suggests: devtools, markdown, renv, testthat, BiocManager, knitr, rmarkdown, roxygen2, mockery, covr, magick, BiocStyle License: Artistic-2.0 MD5sum: be192874f16f5bb0826f6671b331495a Package: marr Version: 1.19.0 Depends: R (>= 4.0) Imports: Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, covr License: GPL (>= 3) MD5sum: c289e0b5508a2c3668093306c33d42a4 Package: marray Version: 1.87.0 Depends: R (>= 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MASS License: GPL (>= 2) MD5sum: e65be8067005b7cb1f468f521e0d81b9 Package: maskBAD Version: 1.53.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) MD5sum: 3ee07f4074ed83552a19c54f6a132931 Package: MassArray Version: 1.61.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: f1661e78c69705e8f0be7745b68683ed Package: massiR Version: 1.45.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: c9c7c5c5b856447676cc246a167b1e6b Package: MassSpecWavelet Version: 1.75.1 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench License: LGPL (>= 2) MD5sum: 46844ca7f3cc754f38ba36b651ddb8b8 Package: mastR Version: 1.9.1 Depends: R (>= 4.3.0) Imports: AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr, graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb, org.Hs.eg.db, patchwork, SeuratObject, 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purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif (>= 1.9.3), xml2 Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: bba2680a8eefa3a2a888fe83321e3804 Package: Mergeomics Version: 1.37.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8cf4abde8bef55d4cd5228a3dc889c4e Package: MeSHDbi Version: 1.45.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: e0363e139d919e7adea2e9b0479b1de5 Package: meshes Version: 1.35.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, DOSE, enrichplot, GOSemSim (>= 2.31.2), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5) Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: 5898d259672d0ff9e50056942cb93a2a Package: meshr Version: 2.15.0 Depends: R (>= 4.1.0) Imports: markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils, fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite License: Artistic-2.0 MD5sum: 291cb47d7cd1da4e780471518e66dd72 Package: MesKit Version: 1.19.0 Depends: R (>= 4.0.0) Imports: methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape (>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges, circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3), ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 53d9d80878d6c9d0d647c8ad8e4dbc57 Package: messina Version: 1.45.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: be43724157b1edbc5dc0c7360c8bc90b Package: metabCombiner Version: 1.19.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: ee25ae6370487fd35e94dd9b984284da Package: metabinR Version: 1.11.0 Depends: R (>= 4.3) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: efee2075d8b15a5df262aff4ce54c72a Package: MetaboAnnotation Version: 1.13.1 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.17.6), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 MD5sum: af77eab78267328f393861a8a289a0e7 Package: MetaboCoreUtils Version: 1.17.1 Depends: R (>= 4.0) Imports: utils, MsCoreUtils, BiocParallel, methods, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, robustbase License: Artistic-2.0 MD5sum: 7ea4d61b9205bf6545f0ac0c05a6b48f Package: MetaboDynamics Version: 1.1.10 Depends: R (>= 4.4.0) Imports: dplyr, ggplot2, KEGGREST, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.4.0), S4Vectors, stringr, SummarizedExperiment, tidyr, dynamicTreeCut, rlang, ape, ggtree, patchwork LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: f5b7f39bd274ae4dfefe4851e10dcd7f Package: metabomxtr Version: 1.43.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: cecbd307af10b7f29a88273e13d6e04d Package: MetaboSignal Version: 1.39.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 201c514463c3d07e496071c32df3b82e Package: metaCCA Version: 1.37.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 400b68e2c28c7d8b3e2fd8a5978ec80f Package: MetaCyto Version: 1.31.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: 8fd531f9d046340ab8414cd230c81fe8 Package: MetaDICT Version: 0.99.4 Depends: R (>= 4.2.0) Imports: stats, RANN, igraph, vegan, edgeR, ecodist, ggplot2, viridis, ggpubr, ape, cluster, matrixStats Suggests: BiocStyle, knitr, rmarkdown, DT, ggraph, tidyverse, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: cd40e3be2707390af9f11747df1e3bdc Package: metagene2 Version: 1.25.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: d8cd472e849d4ddf5be4d6772be2b3ce Package: metagenomeSeq Version: 1.51.0 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 2c2ab0a1ff1f98b32c7a07b5ec65a613 Package: metahdep Version: 1.67.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 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BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: a4b69cd468a835c900d94debfb10c383 Package: metaSeq Version: 1.49.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 4793011113f9b5d343c1c0512f5b55ff Package: metaseqR2 Version: 1.21.2 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, txdbmaker, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 7efc964c06fc7a9592758095a52889de Package: MetCirc Version: 1.39.0 Depends: R (>= 4.4), amap (>= 0.8), circlize (>= 0.4.16), scales (>= 1.3.0), shiny (>= 1.8.1.1), Spectra (>= 1.15.3) Imports: ggplot2 (>= 3.5.1), MsCoreUtils (>= 1.17.0), S4Vectors (>= 0.43.1) Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) License: GPL (>= 3) MD5sum: 1cdb8047e4af588acf1434ac93f2f513 Package: methimpute Version: 1.31.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 6a5554241b09e6ccc30a9a7f02a5aafb Package: methInheritSim Version: 1.31.1 Depends: R (>= 3.5.0) Imports: methylKit, GenomicRanges, Seqinfo, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 MD5sum: 32fbc9aef5a2a915085d112a57f4676c Package: MethPed Version: 1.37.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 2b5586c1029db2ca0846784b79096b40 Package: MethReg Version: 1.19.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite, TFBSTools Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils, doParallel, reshape2, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, data.table, downloader License: GPL-3 MD5sum: b0495f8283cb8b6710d0dacbc2b7d4e0 Package: methrix Version: 1.23.1 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 8d633a20bf591b6a471f52396164ddb7 Package: MethTargetedNGS Version: 1.41.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: fffd3986b6f35b318f84b742e74cd16e Package: MethylAid Version: 1.43.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 469c8de6f15c564309a4695d64dfecd9 Package: methylCC Version: 1.23.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 3c26bba2fc1d650bb3ade92361141fcb Package: methylclock Version: 1.15.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: 4f58a0c116f78fd0313ed637c85d5b4e Package: methylGSA Version: 1.27.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: b88e4933718f5cba2016ecbf136e5481 Package: methyLImp2 Version: 1.5.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 833d8b7bfa5114b708a21a0bc60241de Package: methylInheritance Version: 1.33.1 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 54c740943a7497b1e13d8097b2755b89 Package: methylKit Version: 1.35.1 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), Seqinfo, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1) Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: 209ce2b8d44afe76827ad7c8e7a430c3 Package: MethylMix Version: 2.39.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 7185826b7a5eef0b9a4a3832063a5be0 Package: methylMnM Version: 1.47.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: f41007c15746a080f860a836780b8905 Package: methylPipe Version: 1.43.1 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, Seqinfo, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 9ce08c7cf550769e0ef34f67463eeda9 Package: methylscaper Version: 1.17.0 Depends: R (>= 4.4.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: 2f418b2e9c5efbb48c148a4a1019a900 Package: MethylSeekR Version: 1.49.3 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2), GenomeInfoDb Suggests: BSgenome.Hsapiens.UCSC.hg38 License: GPL (>= 2) MD5sum: eaa1a80e8d5393026ce36d6f11e40f0d Package: methylSig Version: 1.21.2 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, Seqinfo, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: ab3d1f081ee4545b7e8b1a718698db79 Package: methylumi Version: 2.55.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: 45243f3468523b15e0dcdeb9de842ce3 Package: MetID Version: 1.27.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: 367e75e22c430287382014511fd58ab3 Package: MetNet Version: 1.27.1 Depends: R (>= 4.1), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 4.1), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 4.1), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: ff50add7f6ab3e1262151b8f05d7a14d Package: Mfuzz Version: 2.69.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: b17ee72beb59fabf89402178785aa91e Package: MGFM Version: 1.43.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: e99a169a4c23b7efb67ab2657228b388 Package: mgsa Version: 1.57.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: f716def72d70c350c385217703e9394c Package: miaSim Version: 1.15.1 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: 3b628bd01b2044a1fbfc8a1ec6b4a00a Package: MiChip Version: 1.63.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 91eb8d1dfbb47ae45ae3f184bb8a56ca Package: microbiome Version: 1.31.4 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: 4c5851ca49860a34d408a1d1235efe78 Package: microbiomeDASim Version: 1.23.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 12984210e03332df39695a3b05cd7268 Package: microbiomeExplorer Version: 1.19.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 3b9e4d1a6ac382e4efda7c216200617a Package: MicrobiomeProfiler Version: 1.15.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 81863fc1e9d6895846deb3f027cd9330 Package: MicrobiotaProcess Version: 1.21.2 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) MD5sum: e80e7f6bb6e0d7932fe2208d66a0d8d1 Package: microRNA Version: 1.67.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 89a9cce4adf6f303e3de8bbc87472e70 Package: MICSQTL Version: 1.7.0 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: e72a81ec1e17d06419d80cacbe0ee06f Package: miloR Version: 2.5.2 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppML Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics, sparseMatrixStats License: GPL-3 + file LICENSE MD5sum: 435ecaebd52b807a17cccee47273e6ae Package: mimager Version: 1.33.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: d6ff47b6b7991a8ecf7d4367cbd1d3ab Package: mina Version: 1.17.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: 3c10ba155d498f2f309a4a930b247823 Package: MineICA Version: 1.49.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: c836047d17c4c90c08e89cd57d8af03d Package: minet Version: 3.67.0 Imports: infotheo License: Artistic-2.0 MD5sum: 55b963b6fb3cc94e00a672e8497253e3 Package: minfi Version: 1.55.1 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), bumphunter (>= 1.1.9) Imports: S4Vectors, Seqinfo, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 98ff06aa2ac0c409128c1f535ba75e95 Package: MinimumDistance Version: 1.53.1 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, Seqinfo, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 0b543bfd4ac344abeef9f2b9af36c7d1 Package: MiPP Version: 1.81.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: d341ea3ce725ecb2884204a5e9359fc2 Package: miQC Version: 1.17.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 2d3dcd36bf14ce04beda5b3c083ac71c Package: MIRA Version: 1.31.0 Depends: R (>= 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utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: d1511ea1211d46eecf22c3e1759098d4 Package: mirIntegrator Version: 1.39.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 5859711ce1c9ccfb3bd2687560be18c6 Package: MIRit Version: 1.5.2 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 875b0e41b4642c6cdd26f3834b51aecc Package: miRLAB Version: 1.39.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 7e47a29fccf66b018ab11d5e2872d3ec Package: miRNAmeConverter Version: 1.37.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: f60a9bfcbfe6c1babb66cb29261dadaa Package: miRNApath Version: 1.69.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 54752193d81ce64ce3960487d14cad08 Package: miRNAtap Version: 1.43.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 0d7d7b57dbf0d0764c7624f540b251bd Package: miRSM Version: 2.5.4 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer, grid, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, methods, rJava, BiBitR, rqubic, Biobase, PMA, stats, dbscan, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: c9a43e8da21e61211ac8cdc7d696f0c8 Package: miRspongeR Version: 2.13.4 Depends: R (>= 4.4.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, utils, Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: bcb96b9e902d81cf1e9cc31e28edb061 Package: mirTarRnaSeq Version: 1.17.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: abcc9d036916831d309dbc64ba704994 Package: missMethyl Version: 1.43.1 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomeInfoDb, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 3661bd042267609198c3dc55048e8f0e Package: missRows Version: 1.29.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: ada8d1ff4629a0e4dc4eb6a4f154c628 Package: mist Version: 1.1.0 Depends: R (>= 4.5.0) Imports: BiocParallel, MCMCpack, Matrix, S4Vectors, methods, rtracklayer, car, mvtnorm, SummarizedExperiment, SingleCellExperiment, BiocGenerics, stats, rlang Suggests: knitr, rmarkdown, RUnit, ggplot2, BiocStyle License: MIT + file LICENSE MD5sum: f5a9f9e7ce638afe9d2aaa7be2912234 Package: mitch Version: 1.21.3 Depends: R (>= 4.4) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra, dplyr, network Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: b144a1f83cdbc2b520c3cc73f507aae8 Package: mitoClone2 Version: 1.15.1 Depends: R (>= 4.4.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 1b3312a8ee3f67985aac42b1917405e9 Package: mixOmics Version: 6.33.0 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils, gsignal, rgl Suggests: BiocStyle, knitr, rmarkdown, mime, testthat, microbenchmark, magick, vdiffr, kableExtra, devtools License: GPL (>= 2) MD5sum: dba7bf5d7d8b33703c5c74cd0224ae57 Package: MLInterfaces Version: 1.89.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL MD5sum: b19339a21b11f82f686a6479579a2e11 Package: MLSeq Version: 2.27.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 00ced34e2e0ca7a9cf47871ac9c80705 Package: MMDiff2 Version: 1.37.1 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: eb765fb956f44d7f7f7f27a1fd23c9b7 Package: mnem Version: 1.25.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: 94434835e5616f6c57272c33ca7e5906 Package: moanin Version: 1.17.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: a6ceb6d7e6a40a8f3c69d291116a7771 Package: mobileRNA Version: 1.5.1 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, Seqinfo, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 188c575e9904b04b8a46358d1fb77fe9 Package: MODA Version: 1.35.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: df2972e5b39d0b539089756250acd4a4 Package: ModCon Version: 1.17.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: ef3e13624653fb915d2bdc4a7a29c6f8 Package: Modstrings Version: 1.25.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 1bed62f5e5c783660cc4db29b652f4cc Package: MOGAMUN Version: 1.19.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 22bce245669e965257ec1ff0b5fd1eba Package: mogsa Version: 1.43.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 8493a23b143b5b8ad0845cdf8ec6eca2 Package: MoleculeExperiment Version: 1.9.0 Depends: R (>= 4.1.0) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6aa3d8252c697606bc4cae31cf0630c4 Package: MOMA Version: 1.21.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 782a3fac74f432d477d8cbdfbb350037 Package: monaLisa Version: 1.15.3 Depends: R (>= 4.1) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap (>= 2.11.1), Seqinfo, GenomicRanges, cli, ggplot2 (>= 4.0.0), glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector Suggests: BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 3) MD5sum: 6c2a80517d5587b117107232007886f0 Package: monocle Version: 2.37.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: d088db37e03e92d37a04a4446c4701ec Package: Moonlight2R Version: 1.7.4 Depends: R (>= 4.5), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub, rlang, withr, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: 90529f6cfe22d7755bd7fdafe1327743 Package: MoonlightR Version: 1.35.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: 084c4a408b96597f32f0132b286bab2c Package: mosaics Version: 2.47.1 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, Seqinfo, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 9c22156a37ee76a4e49c1155353d5eeb Package: mosbi Version: 1.15.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 3179270e1e7656887778c7247e2fa3d9 Package: MOSClip Version: 1.3.3 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 0322b9fb5efa6c269d881a71e48a083e Package: mosdef Version: 1.5.1 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: 30355433326ce95295096a8f03d5b08b Package: MOSim Version: 2.5.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 MD5sum: fd0b114fb9ea72c88c84c41289873b50 Package: Motif2Site Version: 1.13.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: fbc4eec2480e2b31adbe18f7f7ef79ee Package: motifbreakR Version: 2.23.0 Depends: R (>= 4.4.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny, vroom Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38 License: GPL-2 MD5sum: ef8dbcc8ab0f437a1962e0933fdf8adb Package: motifcounter Version: 1.33.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: d823b89718692638ef6a65a4553df10d Package: MotifDb Version: 1.51.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: f99412e0701435ae4ee21943ca01a243 Package: motifmatchr Version: 1.31.1 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, Seqinfo LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: 0db7365e9d5ccfd1ec66db57176962f6 Package: MotifPeeker Version: 1.1.3 Depends: R (>= 4.4.0) Imports: BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, Seqinfo, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, downloadthis, knitr, markdown, methods, remotes, rworkflows, testthat (>= 3.0.0), withr, emoji, curl, jsonlite License: GPL (>= 3) MD5sum: e85a8cbdae7b3b41f91f994b6437c338 Package: motifStack Version: 1.53.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) MD5sum: 399851683ef50d605383aa92850d9b3f Package: motifTestR Version: 1.5.3 Depends: Biostrings, GenomicRanges, ggplot2 (>= 4.0.0), R (>= 4.5.0), Imports: Seqinfo, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif, Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MASS, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0), VGAM License: GPL-3 MD5sum: 7bdd028fecd473bd996869c8d38a0f1d Package: MouseFM Version: 1.19.1 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, Seqinfo, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 8e5b4941d9b8b8e24e45894649c70bec Package: MPAC Version: 1.3.1 Depends: R (>= 4.4.0) Imports: data.table (>= 1.14.2), SummarizedExperiment (>= 1.30.2), BiocParallel (>= 1.28.3), fitdistrplus (>= 1.1), igraph (>= 1.4.3), BiocSingular (>= 1.10.0), S4Vectors (>= 0.32.3), SingleCellExperiment (>= 1.16.0), bluster (>= 1.4.0), fgsea (>= 1.20.0), scran (>= 1.22.1), ComplexHeatmap (>= 2.16.0), circlize (>= 0.4.16), scales (>= 1.3.0), stringr (>= 1.5.1), viridis (>= 0.6.5), ggplot2 (>= 3.5.1), ggraph (>= 2.2.1), survival (>= 3.7), survminer (>= 0.4.9), grid, stats Suggests: rmarkdown, knitr, svglite, bookdown(>= 0.34), testthat (>= 3.0.0) License: GPL-3 MD5sum: c84d893c4dfe321429249a2f47bcb36b Package: MPFE Version: 1.45.0 License: GPL (>= 3) MD5sum: eb89365c37fa0c49b71f297c8f46db99 Package: mpra Version: 1.31.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 17bab6928a8ad604ef4337e7f3281787 Package: MPRAnalyze Version: 1.27.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: 8dc22c14f57be50cd647806c376f0cb3 Package: msa Version: 1.41.3 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) MD5sum: 38b4933313bee923a2d0201f88655bc2 Package: MSA2dist Version: 1.13.0 Depends: R (>= 4.4.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: 89c07e5cf8403e0913cbfabb18d63710 Package: MsBackendMassbank Version: 1.17.1 Depends: R (>= 4.0), Spectra (>= 1.15.10) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 MD5sum: 0b79facf1c123ed7540e45a1e95ff5cc Package: MsBackendMetaboLights Version: 1.3.1 Depends: R (>= 4.2.0), Spectra (>= 1.15.12) Imports: curl, ProtGenerics, BiocFileCache, S4Vectors, methods, progress Suggests: testthat, rmarkdown, mzR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 0abab86807c73e8f048b9ed361e4d745 Package: MsBackendMgf Version: 1.17.0 Depends: R (>= 4.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: 7b2249ccfe7c95cc94db51d694608c2e Package: MsBackendMsp Version: 1.13.0 Depends: R (>= 4.1.0), Spectra (>= 1.5.14) Imports: ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: 664b51bf57ff14a4fc5c54ba77c49fa0 Package: MsBackendRawFileReader Version: 1.15.1 Depends: R (>= 4.1), methods, Spectra (>= 1.15.10) Imports: ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.17.2), utils, BiocParallel Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: 2297852c99c7dff4b876ff147ec46abc Package: MsBackendSql Version: 1.9.2 Depends: R (>= 4.2.0), Spectra (>= 1.19.8) Imports: BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3), DBI, MsCoreUtils, IRanges, data.table, progress, stringi, fastmatch, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR License: Artistic-2.0 MD5sum: 617808dd898f42a3dc7ee541d2b20588 Package: MsCoreUtils Version: 1.21.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest Enhances: HDF5Array License: Artistic-2.0 MD5sum: 724af37e5ea828591ea5ed1f7c9403b5 Package: MsDataHub Version: 1.9.0 Imports: ExperimentHub, utils Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) License: Artistic-2.0 MD5sum: b988998532e8e568e01c8276e2371d23 Package: MsExperiment Version: 1.11.1 Depends: R (>= 4.2), ProtGenerics (>= 1.35.2), Imports: methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures, DBI, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite License: Artistic-2.0 MD5sum: 11ede6909aaf998393dd70e3dd1f19c0 Package: MsFeatures Version: 1.17.1 Depends: R (>= 4.0) Imports: methods, ProtGenerics (>= 1.23.5), MsCoreUtils, SummarizedExperiment, stats Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 4136266cf3293ca539650d4b51795fa1 Package: msgbsR Version: 1.33.1 Depends: R (>= 3.5.0), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, Seqinfo, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: 4b1f3e154d55f8593b72a5acc327311f Package: msImpute Version: 1.19.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) MD5sum: 98bbd25ea947deb4494f1fa03b1cb1a0 Package: msmsEDA Version: 1.47.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: 96da7946b687896138213c68c04a581b Package: msmsTests Version: 1.47.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue Suggests: xtable License: GPL-2 MD5sum: 541e084d85989ca2a584d78a91922542 Package: MSnbase Version: 2.35.2 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.29.3), S4Vectors, ProtGenerics (>= 1.29.1) Imports: MsCoreUtils, PSMatch (>= 1.13.2), BiocParallel, IRanges (>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick, msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment, Spectra License: Artistic-2.0 MD5sum: ef1bd1b845f3bb8f7a6638d4a0882caf Package: mspms Version: 1.1.0 Depends: R (>= 4.4.0) Imports: QFeatures, limma, SummarizedExperiment, magrittr, rlang, dplyr, purrr, stats, tidyr, stringr, ggplot2, ggseqlogo, heatmaply, readr, rstatix, tibble, ggpubr Suggests: knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown, BiocStyle, imputeLCMD License: MIT + file LICENSE MD5sum: 97ce76631d25a167f53223c407a04489 Package: msqrob2 Version: 1.17.1 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, MsDataHub, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 MD5sum: 4d15f117bb243332688ce5b1561cacdb Package: MsQuality Version: 1.9.2 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata (>= 0.32.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics (>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.7.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra (>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 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License: file LICENSE MD5sum: 7bf665330021ef518667fd9cebe9a08c Package: MSstatsConvert Version: 1.19.3 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils, stringi, Rcpp, parallel LinkingTo: Rcpp Suggests: tinytest, covr, knitr, arrow, rmarkdown License: Artistic-2.0 MD5sum: fda980d4602e381bf14fefaf832964cf Package: MSstatsLiP Version: 1.15.3 Depends: R (>= 4.1) Imports: dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats, plotly, htmltools LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight License: Artistic-2.0 MD5sum: e62bf5132fc0c980bab8a3961fac542a Package: MSstatsLOBD Version: 1.17.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 MD5sum: ae87a0e6ac1d84b9dff5abf9628e9a1e Package: MSstatsPTM Version: 2.11.5 Depends: R (>= 4.3) Imports: dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools LinkingTo: Rcpp Suggests: knitr, rmarkdown, tinytest, covr, mockery, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 6c7ab69ff9af54100017793c4aa684c4 Package: MSstatsQC Version: 2.27.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: c1111f1ebb2bc76ee1c74fe7e5b369e5 Package: MSstatsQCgui Version: 1.29.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: 72193704b0efebced7d34a72df789cf5 Package: MSstatsShiny Version: 1.11.5 Depends: R (>= 4.2) Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery, MSstatsBioNet, shinydashboard, arrow, tools Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2, License: Artistic-2.0 MD5sum: 61889138fa278711493b5ec33496a3a1 Package: MSstatsTMT Version: 2.17.0 Depends: R (>= 4.2) Imports: limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 5eab6c3f71ae6850c89da8153503d1bd Package: MuData Version: 1.13.0 Depends: Matrix, S4Vectors, rhdf5 (>= 2.45) Imports: methods, stats, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, DelayedArray, S4Vectors Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater License: GPL-3 MD5sum: 5fc1cc34579a0d02b846d28fbf9afc53 Package: Mulcom Version: 1.59.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 0587dd9d809bf2561ef0d29f530ef93f Package: MultiAssayExperiment Version: 1.35.9 Depends: SummarizedExperiment, R (>= 4.5.0) Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, MatrixGenerics, methods, S4Vectors, tidyr, utils Suggests: BiocStyle, HDF5Array, h5mread, knitr, maftools, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR License: Artistic-2.0 MD5sum: 14f883725d45e07ef61e25085d6f690e Package: MultiBaC Version: 1.19.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: 7f0e5214afdcfbf87db73cffb08f0b30 Package: multiClust Version: 1.39.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: dfe6067a792155d5415f67829020a155 Package: multicrispr Version: 1.19.1 Depends: R (>= 4.0) Imports: BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, GenomeInfoDb, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: f1736eb0b6f359f28c6d22cf3c77980a Package: MultiDataSet Version: 1.37.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: a9aec7504bc35756d81ba895f1f95119 Package: multiGSEA Version: 1.19.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: ff8d4dbb9fe8a0a64d4af6fddfc0ed6a Package: multiHiCcompare Version: 1.27.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: b515acfcb2b7534c54a5e0426baaee7b Package: MultiMed Version: 2.31.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 94efcdfa41eed80757b0a2fb60ff6214 Package: multiMiR Version: 1.31.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: 5bc608dc1e866ca0603590b2bcccc44b Package: MultimodalExperiment Version: 1.9.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e19cd45d1ed9532a189fae79e958f47f Package: multiscan Version: 1.69.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: e706f9fccb63c93237eef6421a0ebbb2 Package: multistateQTL Version: 2.1.2 Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, collapse Imports: methods, S4Vectors, data.table, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices Suggests: testthat, BiocStyle, knitr, covr, rmarkdown License: GPL-3 MD5sum: d535880da0c3c4c2de734c0149489807 Package: multiWGCNA Version: 1.7.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 4d7a792df322159aadd8abdc6c28b350 Package: multtest Version: 2.65.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: a4fad9743837d3ec6e3bfb8a8c9e685c Package: mumosa Version: 1.17.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: 0452a972138a7a97b61038b0c7b0216f Package: MungeSumstats Version: 1.17.5 Depends: R(>= 4.1) Imports: data.table, utils, R.utils, dplyr, stats, GenomicRanges, GenomeInfoDb, IRanges, ieugwasr(>= 1.0.1), BSgenome, Biostrings, stringr, VariantAnnotation, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: c4267173e04c706cccc10074063f030f Package: muscat Version: 1.23.1 Depends: R (>= 4.5) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, IHW, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition Suggests: BiocStyle, cowplot, countsimQC, AnnotationHub, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, tidyr, UpSetR License: GPL-3 MD5sum: b82cdf621fef3773229b8dd36e2b52e3 Package: muscle Version: 3.51.0 Depends: Biostrings License: Unlimited MD5sum: 18f63ba887906e513aebbad8da346995 Package: musicatk Version: 2.3.2 Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1), scales Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: 538164fc9cc58894e8bdb1a9d8eb1796 Package: mutscan Version: 0.99.2 Depends: R (>= 4.5.0) Imports: BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp, edgeR (>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally, ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw, rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray, tools LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign, plotly, scattermore, BiocManager License: MIT + file LICENSE MD5sum: ee889da42f615e8ac3dec96b1e5a321c Package: MVCClass Version: 1.83.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 29b907431235d1644d534f43ef7ea395 Package: MWASTools Version: 1.33.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: bd0240d7b9b97a5c8de9267cf2dc5927 Package: mygene Version: 1.45.0 Depends: R (>= 3.2.1), GenomicFeatures, txdbmaker Imports: methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7), Hmisc, sqldf, plyr, S4Vectors Suggests: BiocStyle License: Artistic-2.0 MD5sum: 99a21339f6499cd036bd59034bc5a4d8 Package: myvariant Version: 1.39.1 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, Seqinfo, 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knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: 013c94ab5ad5621d53d249b6067c1942 Package: ncdfFlow Version: 2.55.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr MD5sum: 67f835781f538ebd0d2785101cc33575 Package: ncGTW Version: 1.23.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 MD5sum: da5d4014e381e4dc715cabf93542858d Package: ncRNAtools Version: 1.19.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: 69c55fd9c6fe7a1b1efe46d03210d1b8 Package: ndexr Version: 1.31.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 8d104f563704e076758f55973b1a7832 Package: nearBynding Version: 1.19.1 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, Seqinfo, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 6799f1bba2e633808cf9b6fec369e593 Package: Nebulosa Version: 1.19.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat License: GPL-3 MD5sum: 97e609db5ce051879873ffd2d5d8df26 Package: nempi Version: 1.17.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle License: GPL-3 MD5sum: b33ca542e751d9c3f2822bb6b0b003d9 Package: NetActivity Version: 1.11.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: 5b503e963fb2ce84e776451531cbb71e Package: netboost Version: 2.17.0 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, BiocStyle, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown License: GPL-3 OS_type: unix MD5sum: b75fb30928add70054fecc83f390c274 Package: nethet Version: 1.41.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 6ed8b1ce1dd03580f7f77fb569606fd1 Package: NetPathMiner Version: 1.45.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 0a07521a3434cd3ae5277e80332f112c Package: netprioR Version: 1.35.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: 8418180fce06810f111a63bda83fcf9d Package: netresponse Version: 1.69.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: 10ae1d3299c7bbb2b7b189fb88256c4e Package: NetSAM Version: 1.49.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL MD5sum: 1c9a8c34700d09f99cbc7651aabc51e6 Package: netSmooth Version: 1.29.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: f1b9e99d4b6ae97111995458eb6d859e Package: NewWave Version: 1.19.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: 6e9448837cc427211eff86404631ba64 Package: ngsReports Version: 2.11.1 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 4.0.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 MD5sum: debbf1336cf4512f92bb4d2fe845b95a Package: nipalsMCIA Version: 1.7.0 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 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rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL-3 MD5sum: 28b8a76d7a1e8c6c2a05a366c9dfd36b Package: NoRCE Version: 1.21.2 Depends: R (>= 4.4.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,Seqinfo, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi,methods Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, markdown License: MIT + file LICENSE MD5sum: 4a4792e530bf2e2f5c51b000531775dc Package: normalize450K Version: 1.37.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 6dd805dee4a94d0882759ae067368fef Package: NormalyzerDE Version: 1.27.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: d15ba43826e1cff72c89230d2fbbab11 Package: NormqPCR Version: 1.55.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: fb6f2a6f822e70c0461dd40e4da83c94 Package: normr Version: 1.35.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: c4b8732b175c7fae6132d7f73b683686 Package: notame Version: 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igraph, knitr, notameStats, pcaMethods, Rtsne, testthat License: MIT + file LICENSE MD5sum: ca03af89d61018fad3dcfcb46a434558 Package: NPARC Version: 1.21.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: 47b6b5f9cc11ebbfa6ee75cda15f51aa Package: npGSEA Version: 1.45.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: ff8a3268fb00ecdfe06c9f6533884ccd Package: NTW Version: 1.59.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: ceb3c9d5e9dbd1fd7304c8f9cf56c4df Package: nucleoSim Version: 1.37.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 092c524ec04e5a38eebf0efaa01cae54 Package: nucleR Version: 2.41.1 Depends: R (>= 3.5.0), methods Imports: Biobase, BiocGenerics, Biostrings, Seqinfo, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: b39ddd224f67af47c7e31deade116de0 Package: nuCpos Version: 1.27.0 Depends: R (>= 4.2.0) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 MD5sum: 6cfd8a06feb7beaf0260b538b3c45346 Package: nullranges Version: 1.15.1 Depends: R (>= 4.2.0) Imports: stats, IRanges, GenomicRanges, Seqinfo, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, GenomeInfoDb, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, magrittr, tidyr, cobalt, 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pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 6a9f37b504228a530ef627272eb6b814 Package: oligoClasses Version: 1.71.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 5ef478f4fc4a62376cdbeaa42e2cafb9 Package: OLIN Version: 1.87.0 Depends: R (>= 2.10), 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SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr, nipals Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: fc916d2aec33006e39f177d7b8f6142d Package: oncomix Version: 1.31.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 3cd4ae380e71205b0adbcffe42116a08 Package: oncoscanR Version: 1.11.1 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: ce8bfcfaf17a8bcd9f0903d145602645 Package: OncoScore Version: 1.37.1 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 1d87b6afed37da0bbd38204c3bef708e Package: ontoProc Version: 2.3.11 Depends: R (>= 4.1), ontologyIndex Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr, basilisk, jsonlite, RBGL, ellmer Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick, License: Artistic-2.0 MD5sum: e0c9995245a271eea4a981e2c0f624b0 Package: openCyto Version: 2.21.1 Depends: R (>= 3.5.0) Imports: methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>= 3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices LinkingTo: cpp11, BH(>= 1.62.0-1) Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, 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Suggests: GenomeInfoDb, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: f17b47d5ef4b1a3e43e228f63fca97e3 Package: OrganismDbi Version: 1.51.4 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), Seqinfo, GenomicFeatures (>= 1.61.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.61.1) Suggests: txdbmaker, GenomeInfoDbData, Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 17b925d6c6f618747bde5ab329c4df4c Package: orthogene Version: 1.15.02 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 MD5sum: 27b1438ad31b5ecffe72bbbc05b14a64 Package: orthos Version: 1.7.4 Depends: R (>= 4.3), SummarizedExperiment Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2 (>= 3.4.0), ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras (>= 2.16.0), methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 521d0cc49f19f8fe873399f04b86becf Package: OSAT Version: 1.57.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: b45621acca0eec9923159d2d441ac3b6 Package: Oscope Version: 1.39.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: 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TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase License: file LICENSE MD5sum: 3dc276928f47c480def8edcad8f65f61 Package: OutSplice Version: 1.9.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 12fa6f6f1a70e3a3b2d9fe11caedc9fa Package: OVESEG Version: 1.25.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: fb22a5463faf9cd49bfe8895034e76cb Package: PAA Version: 1.43.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: 9b2acd485500254566b761ac5ee9f894 Package: packFinder Version: 1.21.0 Depends: R (>= 4.1.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 MD5sum: 7a081b6f709721251e2a667adf6236d2 Package: padma Version: 1.19.0 Depends: R (>= 4.1.0), SummarizedExperiment, S4Vectors Imports: FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2 License: GPL (>= 3) MD5sum: 78208dd6a065ebc5e2387b8e25975d1a Package: PADOG Version: 1.51.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: 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BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: a3de9f364af7fe70a7c8e150ecbe9bc0 Package: pathRender Version: 1.77.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: c1ade19d42983430d41cc631773fe803 Package: pathview Version: 1.49.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 491b23832401b3be6add139f389d2279 Package: pathwayPCA Version: 1.25.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: 8ab26c940e0e9d16523f2bbbf3453ab8 Package: 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htmlwidgets, plotly, colourpicker, shinytoastr Suggests: diffviewer, gridExtra, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools, R.devices, usethis, rlang, magick, cowplot License: Artistic-2.0 MD5sum: 9a41c9e871597548b991f5d97e3f2d6b Package: pengls Version: 1.15.2 Depends: R (>= 4.5.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 76406d299269c4213b719d19e3ce15a5 Package: PepSetTest Version: 1.3.0 Depends: R (>= 4.1.0) Imports: dplyr, limma, lme4, MASS, matrixStats, reshape2, stats, tibble, SummarizedExperiment, methods Suggests: statmod, BiocStyle, knitr, rmarkdown, tidyr License: GPL (>= 3) MD5sum: 39eeb31008c23f8969aaa24f30d3f6fd Package: PepsNMR Version: 1.27.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: a8ddfdd56fbe5e4e8f8a8988daaf0e3a Package: pepStat Version: 1.43.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: 4ca13d9604b1ed21d09cd4c3757a6524 Package: pepXMLTab Version: 1.43.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 291dc82fa5081403f66c6c4f41b50128 Package: periodicDNA Version: 1.19.1 Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel Imports: S4Vectors, rtracklayer, stats, Seqinfo, magrittr, zoo, ggplot2, methods, parallel, cowplot Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE MD5sum: c243cd58fec4ec9eee22a0a43e68f218 Package: pfamAnalyzeR Version: 1.9.0 Depends: R (>= 4.3.0), readr, stringr, dplyr Imports: utils, tibble, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 02a96637b4d6c28490444df2df568ad8 Package: pgca Version: 1.33.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: e8c06f1f08c5aef592b68d431b6e93ef Package: pgxRpi Version: 1.5.5 Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel, future, future.apply Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 MD5sum: 75345090944c4a279f8fc1d576cbb61a Package: PharmacoGx Version: 3.13.2 Depends: R (>= 4.1.0), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: 8f54f704eb364371d628a543bb2754ea Package: PhenoGeneRanker Version: 1.17.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: d12e86882462ca643bc8b1f01657e283 Package: phenomis Version: 1.11.0 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 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GPL-3 MD5sum: 52892fbfe243ee5d809f1e728be15e60 Package: PhIPData Version: 1.17.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: 5a64216812f9fdc4edac28b58b93e6b1 Package: phosphonormalizer Version: 1.33.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: c238e5bf135beb6ebbdfb98421532ffb Package: PhosR Version: 1.19.2 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: f5cc92ef88f7841422051363c3b23bc3 Package: PhyloProfile Version: 2.1.12 Depends: R (>= 4.5.0) Imports: ape, bioDist, BiocStyle, Biostrings, bsplus, colourpicker, data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra, htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast, scattermore, shiny, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, svglite, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 7864e00703262eeb757ece4d429dc242 Package: piano Version: 2.25.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 8e60c4603e44b0fceb01906f63a966d4 Package: PICB Version: 1.1.1 Imports: utils, Seqinfo, GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr, S4Vectors, methods Suggests: GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle, prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6, BiocManager, rmarkdown, ggplot2 License: CC0 MD5sum: 4002b9afd05ca660c13725e47adcc35f Package: pickgene Version: 1.81.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 4050489d4bb80869c3a267c8ad46445a Package: pipeComp Version: 1.19.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: 52e7c858cd141f5e92dc08a780b909c5 Package: pipeFrame Version: 1.25.1 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, Seqinfo, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: d7e53ca040eaa9d6254428ff11af9eb3 Package: PIPETS Version: 1.5.0 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 9c4b1a32b9b4a9e45d0d0df982bbb3fa Package: PIUMA Version: 1.5.0 Depends: R (>= 4.3), ggplot2 Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 + file LICENSE MD5sum: d7f10613627f5be4669836dafa867574 Package: planet Version: 1.17.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ExperimentHub, mixOmics, ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: 34f3bad3b06006047696755bc8e9f7ce Package: planttfhunter Version: 1.9.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6fc4a44d2836013123ff830a3fa24218 Package: plasmut Version: 1.7.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 0394a5b62311c99c16c0aa15707a0f4c Package: plgem Version: 1.81.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: 086478ef2ccee4583788b9057f7b7bb8 Package: plier Version: 1.79.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: 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eea019b49cf6a4618d14cc3f77886de8 Package: pram Version: 1.25.1 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), Seqinfo, GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: 4addad36dba7e39c9b0270c325528fb4 Package: prebs Version: 1.49.1 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, Seqinfo, S4Vectors Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 MD5sum: e27e151c7d1f125c58702993e486fcdb Package: preciseTAD Version: 1.19.0 Depends: R (>= 4.1) Imports: S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics, e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW, foreach, pbapply, stats, parallel, gtools, rCGH Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle License: MIT + file LICENSE MD5sum: 10c4c2e57243be191861d1d8f26ce557 Package: PREDA Version: 1.55.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 MD5sum: 25f9fc2100d3a21f9d7cc640ad4f99be Package: preprocessCore Version: 1.71.2 Imports: stats License: LGPL (>= 2) MD5sum: 183192d8bb8f1528e0c2370957f845d8 Package: primirTSS Version: 1.27.0 Depends: R (>= 3.5.0) Imports: GenomicRanges (>= 1.32.2), S4Vectors (>= 0.18.2), rtracklayer (>= 1.40.3), dplyr (>= 0.7.6), stringr (>= 1.3.1), tidyr (>= 0.8.1), Biostrings (>= 2.48.0), purrr (>= 0.2.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1), phastCons100way.UCSC.hg38 (>= 3.7.1), GenomicScores (>= 1.4.1), shiny (>= 1.0.5), Gviz (>= 1.24.0), BiocGenerics (>= 0.26.0), IRanges (>= 2.14.10), TFBSTools (>= 1.18.0), JASPAR2018 (>= 1.1.1), tibble (>= 1.4.2), 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ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) License: GPL-3 MD5sum: b1696baf4bf90734171a02bb4ffa98b7 Package: ProtGenerics Version: 1.41.0 Depends: methods Suggests: testthat License: Artistic-2.0 MD5sum: 3224a1f209ee447f8674525651036daa Package: psichomics Version: 1.35.0 Depends: R (>= 4.0), shiny (>= 1.7.0), shinyBS Imports: AnnotationDbi, AnnotationHub, BiocFileCache, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, 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BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) MD5sum: e275b973a93709201c4edd66d8f0846b Package: qcmetrics Version: 1.47.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown, markdown License: GPL-2 MD5sum: fdc129753c07b1db498f5ff0fbb3dcad Package: QDNAseq Version: 1.45.1 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, BiocGenerics, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), Seqinfo, GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply (>= 1.8.1) Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), 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stats, ggplot2, rlang, methods Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: b32f4f2ef3f67eaa5e5ca998115673b4 Package: QTLExperiment Version: 2.1.2 Depends: SummarizedExperiment Imports: methods, rlang, checkmate, dplyr, collapse, vroom, tidyr, tibble, utils, stats, ashr, S4Vectors, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 MD5sum: 988989ea7469a4f5581107c821a2c4ec Package: Qtlizer Version: 1.23.0 Depends: R (>= 3.6.0) Imports: httr, curl, GenomicRanges, stringi Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 15a8f2ff61df68b7ce7bdab3bca0041d Package: quantiseqr Version: 1.17.0 Depends: R (>= 4.1.0) Imports: Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, 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knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, recount License: Artistic-2.0 MD5sum: 98aa508ae631304bc3a740a910015cbd Package: recountmethylation Version: 1.19.0 Depends: R (>= 4.1) Imports: minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub License: Artistic-2.0 MD5sum: 9441e12b65cbe415c211f9a52f444bbc Package: recoup Version: 1.37.1 Depends: R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap Imports: BiocGenerics, biomaRt, Biostrings, circlize, Seqinfo, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, txdbmaker, utils Suggests: GenomeInfoDb, grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL License: GPL (>= 3) MD5sum: 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Imports: memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, Seqinfo, GenomeInfoDb, S4Vectors, tools Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat License: Artistic-2.0 MD5sum: a527a3f06687dd8f6299c27f9649df11 Package: regioneReloaded Version: 1.11.0 Depends: R (>= 4.2), regioneR Imports: stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e577151b7a983f28e3827f77dfd58413 Package: regionReport Version: 1.43.1 Depends: R(>= 3.2) Imports: BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats, DESeq2, Seqinfo, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 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settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, Seqinfo, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 33e723681cdc4c976f6b0b2f525826b0 Package: ReportingTools Version: 2.49.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 MD5sum: 00621a5506237a9a05a147cf0923d6c6 Package: ResidualMatrix Version: 1.19.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: d86bff1a1046e3abe3a2927218768e21 Package: RESOLVE Version: 1.11.2 Depends: R (>= 4.1.0) Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel, reshape2, S4Vectors, RhpcBLASctl, survival Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 1c134277afa5d3dcc1b15110dacae69a Package: retrofit Version: 1.9.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 MD5sum: 5c92539ff1f33f12110987b6af90072f Package: ReUseData Version: 1.9.0 Imports: Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools, utils, methods, jsonlite, yaml, basilisk Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 365dd55ea08c9ab3e22b1c61bfefb061 Package: rexposome Version: 1.31.0 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown License: MIT + file LICENSE MD5sum: 6a560edb4c758479d4dbbf17caf98b9e Package: rfaRm Version: 1.21.0 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors, jsonlite Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: 756a7d797f9bc7d5cfa63c9cd7569261 Package: rfPred Version: 1.47.1 Depends: R (>= 3.5.0), methods Imports: utils, Seqinfo, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) MD5sum: 7b7b3a59938d6fafccf4ff4d572e1b91 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stringr, stringi, ggplot2, tibble, lipidr License: MIT + file LICENSE MD5sum: 1ad932bcfc2afe1859dcb2dd618ba525 Package: RGraph2js Version: 1.37.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 MD5sum: bc1a312e44d94dcbef48b7e4180c8983 Package: Rgraphviz Version: 2.53.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: fd9b7ee8482b897c426397af48a3419f Package: rGREAT Version: 2.11.0 Depends: R (>= 4.0.0), GenomicRanges, IRanges, methods Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE MD5sum: cd150c9bcdec7015191d3f34a8eecc43 Package: RGSEA Version: 1.43.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: 8b89861c07084ee4cc2d437c617da453 Package: rgsepd Version: 1.41.0 Depends: R (>= 4.2.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 MD5sum: 21ed3c3a62771871d327ee8dedda4eb3 Package: rhdf5 Version: 2.53.6 Depends: R (>= 4.0.0), methods Imports: Rhdf5lib (>= 1.13.4), rhdf5filters (>= 1.15.5) LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel License: Artistic-2.0 MD5sum: c31bd2c2ce191ef419a7af437b795bc7 Package: rhdf5filters Version: 1.21.0 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7) License: BSD_2_clause + file LICENSE MD5sum: 9b9a714d50f0e2f74ce8437d9c636862 Package: Rhdf5lib Version: 1.31.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 MD5sum: 73eb983c4696a1b2049a118cc54a2b26 Package: Rhisat2 Version: 1.25.0 Depends: R (>= 4.4.0) Imports: txdbmaker, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 MD5sum: 31f7aba2f9018371fc08a2f6e69f24de Package: Rhtslib Version: 3.5.0 Imports: tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL (>= 2) MD5sum: 6098dad45d2cd6d4960fe456cb6cbf1c Package: RiboCrypt Version: 1.15.4 Depends: R (>= 3.6.0), ORFik (>= 1.13.12) Imports: bslib, BiocGenerics, BiocParallel, Biostrings, ComplexHeatmap, cowplot, crosstalk, data.table, dplyr, DT, fst, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, grid, htmlwidgets, httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly, rlang, rclipboard, RCurl, rtracklayer, shiny, shinycssloaders, shinyhelper, shinyjs, shinyjqui, shinyWidgets, stringr, writexl Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 74858eb6f00c3e4df0c1372a662533e6 Package: RiboDiPA Version: 1.17.1 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache, BiocGenerics, txdbmaker LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 9a574feda9b9d9cfb2d5111d8edeae86 Package: RiboProfiling Version: 1.39.1 Depends: R (>= 3.5.0), Biostrings Imports: methods, BiocGenerics, Seqinfo, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 81bda6a7e3764d15469e154eaa66df6a Package: ribor Version: 1.21.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 581d1b07af57a675b2a66deb8afe38b7 Package: riboSeqR Version: 1.43.1 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, S4Vectors, baySeq, Seqinfo, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: b01725111478553f08fdf0619d926bb4 Package: ribosomeProfilingQC Version: 1.21.2 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, Seqinfo, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid, txdbmaker, ggExtra Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, GenomeInfoDbData, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase License: GPL (>= 3) + file LICENSE MD5sum: 373aca7878fe1d4351d89c487d8b4ece Package: rifi Version: 1.13.1 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 251135fe0d7fc817428fcf39a2e46509 Package: rifiComparative Version: 1.9.0 Depends: R (>= 4.2) Imports: cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: ba1adfea60c79ea6704214d124a7a83b Package: Rigraphlib Version: 1.1.2 LinkingTo: biocmake Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 7695175d3b46816a1724144a455445d4 Package: rigvf Version: 1.1.3 Depends: R (>= 4.1.0) Imports: methods, httr2, rjsoncons, dplyr, tidyr, rlang, memoise, cachem, whisker, jsonlite, GenomicRanges, IRanges, Seqinfo Suggests: knitr, rmarkdown, testthat (>= 3.0.0), plyranges, plotgardener, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene License: MIT + file LICENSE MD5sum: 9b800c58d4a3a3aeef3114fba35ce2c4 Package: RImmPort Version: 1.37.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 89142c5ef226505923f09b304fdf8750 Package: RITAN Version: 1.33.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE MD5sum: a2b06dfabd2495362814fbff6487ab2f Package: RIVER Version: 1.33.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: a0b759055f665bd50603af0fd6959be4 Package: RJMCMCNucleosomes Version: 1.33.2 Depends: R (>= 3.5), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, Seqinfo, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: 162faecf23b0e5a21482b14a10eb7eb1 Package: RLassoCox Version: 1.17.0 Depends: R (>= 4.1), glmnet Imports: Matrix, igraph, survival, stats Suggests: knitr License: Artistic-2.0 MD5sum: a76fbdd23ec556b4736a3847617a30f6 Package: RLMM Version: 1.71.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: 2d273eccc179e37ff9f64c3c55fd8d49 Package: Rmagpie Version: 1.65.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) MD5sum: 04e71c2e252816b530bd6de136a44b13 Package: RMassBank Version: 3.19.0 Depends: R (>= 4.1.0), Rcpp Imports: assertthat, Biobase, ChemmineR, data.table, digest, dplyr, enviPat, glue, httr, httr2, logger, methods, MSnbase, mzR, purrr, R.utils, rcdk, readJDX, readr, rjson, S4Vectors, tibble, tidyselect, webchem, XML, yaml Suggests: BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown, RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1) License: Artistic-2.0 MD5sum: 18d87e7d7a3f71d0fdeb117299cdcfe5 Package: rmelting Version: 1.25.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.9-8) Suggests: readxl, knitr, rmarkdown, 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MD5sum: 1250611f44abd0b607843ed5033ccc5b Package: RNAmodR.ML Version: 1.23.0 Depends: R (>= 3.6), RNAmodR Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 MD5sum: 74ec9b4783d152ba8053eff7405720e3 Package: RNAmodR.RiboMethSeq Version: 1.23.1 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Seqinfo, RNAmodR.Data License: Artistic-2.0 MD5sum: e6b83f6b9bc377da79fd5fd23ed2efe9 Package: RNAsense Version: 1.23.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 7854b0664b2c37469053b797ece04e1b Package: rnaseqcomp Version: 1.39.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods 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org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 MD5sum: ec89a9694f496d1952ff79fc3cb5917d Package: Rnits Version: 1.43.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: 3bf3d04c54e8779ca05dc1782d6e8772 Package: roar Version: 1.45.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: 1cc9997b14d3f404dc37e214a033604d Package: roastgsa Version: 1.7.0 Depends: R (>= 4.3.0) Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, 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wordcloud, shiny, grDevices, grid, stats, methods, umap Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 73f436967d0e4fe6a41aab65c5b27da8 Package: Rsamtools Version: 2.25.3 Depends: R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 3c460cc949e4bd7a4b73fd2446ac2983 Package: rScudo Version: 1.25.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: 205ac9f806c286d18227bd03dded0223 Package: rsemmed Version: 1.19.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 71b6a21e12301dcaec0c6800bdf31e1b Package: RSeqAn Version: 1.29.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 5f0a5e7af0552a07fd6b5dc5f0c17fd3 Package: Rsubread Version: 2.23.6 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: 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pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 MD5sum: 1163ecd2a23aa03b5e8de4fea5a605c9 Package: RTCGAToolbox Version: 2.39.1 Depends: R (>= 4.3.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, Seqinfo, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors, stats, stringr, SummarizedExperiment, TCGAutils, utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: 337600c608d202ae2e0ce4fd00edf75b Package: RTN Version: 2.33.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 144f830625611a99b5e8eb6b1a234f79 Package: RTNduals Version: 1.33.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 50cab3411f7ac5463c937eb217f86707 Package: RTNsurvival Version: 1.33.1 Depends: R(>= 4.4.0), RTN(>= 2.29.1), RTNduals(>= 1.29.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 3284e420a79cf05b8b24e552ff21b5e7 Package: RTopper Version: 1.55.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: 1a71702dec3304c0b2fb1c8b0ae0442d Package: Rtpca Version: 1.19.1 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: 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rmarkdown License: GPL-3 MD5sum: ecbc68b28c8f5177458c2b57a65c7606 Package: rTRMui Version: 1.47.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: a2edef213487185168ecfb65e2495765 Package: RUCova Version: 1.1.0 Depends: R (>= 4.4.0) Imports: dplyr, fastDummies, ggplot2, stringr, tibble, Matrix, ComplexHeatmap, grid, circlize, SingleCellExperiment, SummarizedExperiment, tidyverse, tidyr, magrittr, S4Vectors Suggests: knitr, rmarkdown, BiocManager, BiocStyle, remotes, ggpubr, ggcorrplot, ggh4x, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1f634f5ec661bf9ea9eb790e2ed79e78 Package: RUVcorr Version: 1.41.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db, rmarkdown License: GPL-2 MD5sum: 9ba4760236287517a59082ffec7d4985 Package: RUVnormalize Version: 1.43.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: dd4bf4f400c7a528498bc3e277552d3c Package: RUVSeq Version: 1.43.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: 29d34dc3dc9e90f0ffb443563dfda196 Package: Rvisdiff Version: 1.7.0 Depends: R (>= 4.3.0) Imports: edgeR, utils Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager License: GPL-2 | GPL-3 MD5sum: 19b1d60d48360cf92e67ada84eb41d32 Package: RVS Version: 1.31.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: 3d78477f316bbe2648521e6f430a6977 Package: rWikiPathways Version: 1.29.1 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 70bdcdb452496f79974717fbe7c855b9 Package: S4Arrays Version: 1.9.1 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors, IRanges Imports: stats, crayon LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, HDF5Array, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: c814a79880bdb916835b910c0c3ad34d Package: S4Vectors Version: 0.47.4 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.53.2) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 4e5ed6aade450bb4f262ca2b435a7d7c Package: safe Version: 3.49.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 5b2fd4980cf098159c121c8a6521097b Package: sagenhaft Version: 1.79.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: ea0705f37eea80c7f8b003e74fb406cf Package: SAIGEgds Version: 2.9.2 Depends: R (>= 4.0.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.49.6), Rcpp Imports: methods, stats, utils, Matrix, RcppParallel, SKAT, CompQuadForm, survey LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics License: GPL-3 MD5sum: 71fe5243a432d49dc36f5d59dc44a1ee Package: SamSPECTRAL Version: 1.63.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 8397e48d3a731e73ad5564aa05a74808 Package: sangeranalyseR Version: 1.19.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: 7786d582d899ffc12e2b540faff46111 Package: sangerseqR Version: 1.45.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 200d59b96917649171d10b936206e072 Package: SanityR Version: 0.99.3 Imports: Rcpp, BiocGenerics, BiocParallel, MatrixGenerics, methods, S4Vectors, scuttle, SingleCellExperiment, SummarizedExperiment LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), scater, Rtsne License: GPL (>= 3) MD5sum: 330d90ee5908e290b4b71f4a3a58d181 Package: SANTA Version: 2.45.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: c9c59da9c5555cf8396f5a071a28a40a Package: sarks Version: 1.21.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 3709edc519ce99d87ed03f2e7cf8bbe7 Package: saseR Version: 1.5.1 Depends: R (>= 4.3.0) Imports: ASpli, BiocGenerics, BiocParallel, data.table, DESeq2, dplyr, edgeR, GenomicAlignments, GenomicFeatures, GenomicRanges, igraph, IRanges, limma, methods, MASS, MatrixGenerics, S4Vectors, stats, SummarizedExperiment, parallel, PRROC Suggests: rrcov, knitr, txdbmaker License: Artistic-2.0 MD5sum: 37e6fdac4bf3ebb35e363b09f6eb4c81 Package: satuRn Version: 1.17.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: 8c341b964588355c92fa459016f5d224 Package: SBGNview Version: 1.23.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: 67af4ae1429c3ec60fe41825fd9b3994 Package: SBMLR Version: 2.5.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: 92d5f14bbbb2ed5f6e767809179a1cc1 Package: SC3 Version: 1.37.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: 55396c051d5d660466c40689ca6fc256 Package: scafari Version: 0.99.12 Depends: R (>= 4.5.0) Imports: magrittr, shiny, shinycssloaders, DT, dplyr, waiter, ggplot2, tibble, stringr, reshape2, shinyjs, shinyBS, shinycustomloader, factoextra, markdown, plotly, ggbio, GenomicRanges, rhdf5, ComplexHeatmap, biomaRt, org.Hs.eg.db, SummarizedExperiment, SingleCellExperiment, S4Vectors, parallel, httr, jsonlite, scales, tidyr, txdbmaker, circlize, R.utils, dbscan, igraph, RANN Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 807738efc2574a8c99b0b2a86ba823cd Package: Scale4C Version: 1.31.1 Depends: R (>= 3.5.0), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: f1e7639786f541ddec49876db62500b0 Package: ScaledMatrix Version: 1.17.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 MD5sum: 09ffd7a164a6c86cf09acbf535bde678 Package: SCAN.UPC Version: 2.51.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 1a01685eeca27d042dcfec92f9891c23 Package: scanMiR Version: 1.15.1 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, Seqinfo, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 67151da8a69487017796133ad7e84b43 Package: scanMiRApp Version: 1.15.1 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: f5f2c55541bac46af90eae8cdda51db0 Package: scAnnotatR Version: 1.15.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: 554ea078a42f55be4d814caa5ff26768 Package: SCANVIS Version: 1.23.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 3b3f3124acd128395f4ac89b97d469b9 Package: SCArray Version: 1.17.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.36.0), methods, DelayedArray (>= 0.31.5) Imports: S4Vectors, utils, Matrix, SparseArray (>= 1.5.13), BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 MD5sum: 35e95a1afaac5709e5ad756c322d62ed Package: SCArray.sat 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MD5sum: 74dde6ce3525c92152d3500d8d451ef8 Package: scBubbletree Version: 1.11.0 Depends: R (>= 4.2.0) Imports: reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: 91cf580b1c1c7e5356d52ae6a7a20408 Package: scCB2 Version: 1.19.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 7903ce147d111724bca7589d1781d86f Package: scClassify Version: 1.21.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: e2782303e71a6c75d1d4389a0af1e8fc Package: sccomp Version: 2.1.17 Depends: R (>= 4.3.0), instantiate (>= 0.2.3) Imports: stats, boot, utils, scales, lifecycle, rlang, tidyselect, magrittr, crayon, cli, fansi, dplyr, tidyr, purrr, tibble, ggplot2, ggrepel, patchwork, forcats, readr, stringr, glue, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, loo, prettydoc, SeuratObject, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: cfb3751066f3022d6277c9d1db0f7a41 Package: scDataviz Version: 1.19.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 21679d667db9a7266eaf7197d6f4e3f9 Package: scDblFinder Version: 1.23.4 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: e42d6c3de2ebfb6433da36766cc4849b Package: scDD Version: 1.33.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 4a601fe49c2b28aa8e504681dca922a8 Package: scDDboost Version: 1.11.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 4081ef6dce05796ef8864ca1c2de6814 Package: scde Version: 2.37.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 494f6d7da85819e9721860825370579d Package: scDesign3 Version: 1.7.6 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, rvinecopulib, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: 40523fc69c364f36c09dfe932c83a83d Package: scDiagnostics Version: 1.3.0 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, ggplot2, ggridges, SummarizedExperiment, ranger, transport, speedglm, cramer, rlang, bluster, patchwork Suggests: AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 1027396fb276d584d8e3aa84e8ad2a0e Package: scDotPlot Version: 1.3.1 Depends: R (>= 4.4.0) Imports: aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree, grDevices, magrittr, purrr, rlang, scales, scater, Seurat, SingleCellExperiment, stats, stringr, tibble, tidyr Suggests: AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr License: Artistic-2.0 MD5sum: 7591afc0a6d20c4a91ea0aef19c8858c Package: scds Version: 1.25.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: e27f64584b3e96333dd0692210f51f21 Package: SCFA Version: 1.19.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: d75b5fd63c4e4ec538c8d748a1b063ce Package: scFeatureFilter Version: 1.29.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 07587881d90b70abd80f1aa77aa837dd Package: scGPS Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: df5231916cc381c6f5eb2130962326e6 Package: schex Version: 1.23.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: 1557235a4a961c4fc8e1755f70763639 Package: scHiCcompare Version: 1.1.0 Depends: R (>= 4.5.0) Imports: grDevices, graphics, stats, utils, dplyr, ggplot2, gtools, HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix, tidyr, rlang, data.table, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra License: MIT + file LICENSE MD5sum: c8836e90a68c6ebe298b459f31791808 Package: scHOT Version: 1.21.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 829bfcc73d945f26262a1f21041089c2 Package: scider Version: 1.7.2 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, isoband, S4Vectors, grDevices, dbscan, hexDensity, hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 55c1043c1e84be95c19fdf34d838ec6c Package: scifer Version: 1.11.5 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, basilisk.utils, reticulate, here, pwalign, utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: 8f2f4d6f075f70e6b0a8be75b9ea5f42 Package: scmap Version: 1.31.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 286d599979f28fa289f1d3d56d98083e Package: scMerge Version: 1.25.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 MD5sum: b8a4fe71d563c13ba5a204833f582097 Package: scMET Version: 1.11.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: ca8c01533583fce8e90dbf16f950ce63 Package: scMitoMut Version: 1.5.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: 45fabf7a76daad777f7fc3533894bb23 Package: scMultiSim Version: 1.5.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 8f5db06a92b3017d93bed5fc16d2a904 Package: SCnorm Version: 1.31.1 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 02150387e1769ebdb39cf2949c47feda Package: scone Version: 1.33.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats, SparseArray (>= 1.7.6) Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 4cbe5801736e50ace5f4cd7fe947ff0e Package: Sconify Version: 1.29.1 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: e1559c58725d9bb7f3648343b8e80443 Package: SCOPE Version: 1.21.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 571e15c98d0c8d60ebdf19038d11faa3 Package: scoreInvHap Version: 1.31.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 2a90f4860a327dbdd19a5b278aed2900 Package: scoup Version: 1.3.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: 190438d5575822ee4051bdf55c3d4da4 Package: scPCA Version: 1.23.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 7d4a73c0b017edcfcf55c0e733f3d325 Package: scPipe Version: 2.9.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: 222d70de3c784d11f0cff85e8badd082 Package: scran Version: 1.37.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 MD5sum: 9c56806c188701ddf7be39a190138818 Package: scrapper Version: 1.3.13 Imports: methods, Rcpp, beachmat (>= 2.25.1), DelayedArray, BiocNeighbors (>= 1.99.0), Rigraphlib, parallel LinkingTo: Rcpp, assorthead (>= 1.3.10), beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment, SingleCellExperiment, scRNAseq, igraph License: MIT + file LICENSE MD5sum: c7d837a77a7a0849e6ef251cf1adf50f Package: scReClassify Version: 1.15.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: 6c7da9ee4df9c4265aa77f849edd0447 Package: scRecover Version: 1.25.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 269197dc807d0e0a2586300441eed6f4 Package: screenCounter Version: 1.9.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 3f7a00d1de5dd61020592c6ee1dcba3b Package: scRepertoire Version: 2.5.6 Depends: ggplot2, R (>= 4.0) Imports: dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, immApex, iNEXT, Matrix, quantreg, Rcpp, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, SummarizedExperiment, tidygraph, purrr, lifecycle, methods LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, Peptides, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a7ade201bc50bbfdea86a72914a6eb7e Package: scRNAseqApp Version: 1.9.26 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, reshape2, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle, shinytest2 Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 MD5sum: d197c0f5eb7f93b5a0dab6a13c11b2bd Package: scruff Version: 1.27.1 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly, patchwork Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 69078ea9fc9ee178ce6aab246a6a4be2 Package: scry Version: 1.21.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: bc6e1e6dedd504e785b8238377116fde Package: scShapes Version: 1.15.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5b77ffd6f99169f3f2731560b230b28d Package: scTensor Version: 2.19.2 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens License: Artistic-2.0 MD5sum: 0c6eede92219f9c1d17796635996bf46 Package: scTGIF Version: 1.23.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: 11062416749254a91459d03b3c0e709c Package: scTHI Version: 1.21.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 432cb3929c57385e7475a82fc4658cfe Package: scTreeViz Version: 1.15.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: 3b153df0c7030b2837d26d90a2f51813 Package: scuttle Version: 1.19.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: f06fed28b409b0194075f3655a65ac3e Package: SDAMS Version: 1.29.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: b8698fbd3f32d3187480c351a8e21543 Package: seahtrue Version: 1.3.0 Depends: R (>= 4.2.0) Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl (>= 1.0.8), purrr (>= 0.3.5), tidyr (>= 1.3.0), lubridate (>= 1.8.0), stringr (>= 1.4.1), tibble (>= 3.1.8), validate (>= 1.1.1), rlang (>= 1.0.0), glue (>= 1.6.2), cli (>= 3.4.1), janitor (>= 2.2.0), ggplot2 (>= 3.5.0), RColorBrewer (>= 1.1.3), colorspace (>= 2.1.0), forcats (>= 1.0.0), ggridges (>= 0.5.6), readr (>= 2.1.5), scales (>= 1.3.0) Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: ecb5c037b48cc5d422c4d6adcd23e1dc Package: sechm Version: 1.17.1 Depends: R (>= 4.0), SummarizedExperiment, ComplexHeatmap Imports: S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: b4330702d97dee4be6277730023c89da Package: segmenter Version: 1.15.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: a8b01ee09d4d3cf722c08502f50b895b Package: segmentSeq Version: 2.43.1 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: ec7fba0f1c813e11150ba686fa3b4af3 Package: selectKSigs Version: 1.21.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 5be5acd98f76b8de7a95323b0992101f Package: SELEX Version: 1.41.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 983a6a1d670a570d4951da6f1b31caab Package: SemDist Version: 1.43.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 711261271d2d744aabb609e278eb03d9 Package: semisup Version: 1.33.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: c94a32a55be8739fda4a179c97320aed Package: seq.hotSPOT Version: 1.9.0 Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3556ec68259e780f04941848147b11b7 Package: SeqArray Version: 1.49.8 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, Seqinfo, Biostrings LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: 1ba2175e95019bbc351ebdd313364568 Package: seqCAT Version: 1.31.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 9f0bd367b1e30b64a5e34166cea3abb5 Package: seqcombo Version: 1.31.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 8d95ae2e7a4206a0dd0c1cf1d55b4292 Package: SeqGate Version: 1.19.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 394a49d0e0b41f8b2a8f082a19f4c96a Package: SeqGSEA Version: 1.49.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: ddea07dc5b6b0755c20e05baf6c03460 Package: Seqinfo Version: 0.99.2 Depends: methods, BiocGenerics Imports: stats, S4Vectors, IRanges Suggests: GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b417359bfb1347a4309c48b479ca362a Package: seqLogo Version: 1.75.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: b913fe654b25611391088ced5e78db2e Package: seqPattern Version: 1.41.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: ab815d52004aca9b90c1e540c4eacd92 Package: seqsetvis Version: 1.29.1 Depends: R (>= 4.3), ggplot2 Imports: cowplot, data.table, eulerr, Seqinfo, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, GenomeInfoDb, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8192ad294b51b655b7fda24e2faa82e9 Package: SeqSQC Version: 1.31.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: d6911ef2d1eac25d057fa22d3a674b57 Package: SeqVarTools Version: 1.47.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: 21eea088fadcd43d7ba8fb6868b19a54 Package: SEraster Version: 1.1.0 Depends: R (>= 4.5.0) Imports: BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment Suggests: CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager, remotes License: GPL-3 MD5sum: baecee6059d9c35ab19ee0d188304249 Package: sesame Version: 1.27.1 Depends: R (>= 4.5.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1), IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, Seqinfo, stats, SummarizedExperiment (>= 1.39.1), dplyr, reshape2 Suggests: scales, BiocManager, GenomeInfoDb, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: 26696ec959a804cda902eebd83575a6f Package: SETA Version: 0.99.6 Depends: R (>= 4.5.0) Imports: dplyr, MASS, Matrix, SingleCellExperiment (>= 1.30.1), stats, tidygraph, rlang, utils Suggests: BiocStyle, caret, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: d2133db9aabc24f3eda92f47f006faf1 Package: SEtools Version: 1.23.3 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: c5142bac8f6795bd4478d7912da6aacb Package: sevenbridges Version: 1.39.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: 1cd08852ee1754581f69658b526019a0 Package: SGSeq Version: 1.43.1 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), Seqinfo, grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3fc0e2ec701b00cb144be26417024937 Package: SharedObject Version: 1.23.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 514fe9e9c7aed3bcc4a2abcc4320495e Package: shiny.gosling Version: 1.5.0 Depends: R (>= 4.1.0) Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: 8a120b2685a024aaf70697bde7395bae Package: shinybiocloader Version: 0.99.1 Depends: htmltools Imports: shiny Suggests: shinydashboard, tinytest, quarto License: Artistic-2.0 MD5sum: 9b6b5c14ccd110453dcfeed7ac54ee39 Package: shinyDSP Version: 1.1.2 Depends: R (>= 4.5) Imports: AnnotationHub, BiocGenerics, bsicons, bslib, circlize, ComplexHeatmap, cowplot, dplyr, DT, edgeR, ExperimentHub, ggplot2, ggpubr, ggrepel, grDevices, grid, htmltools, limma, magrittr, pals, readr, S4Vectors, scales, scater, shiny, shinycssloaders, shinyjs, shinyvalidate, shinyWidgets, SingleCellExperiment, standR, stats, stringr, SummarizedExperiment, tibble, tidyr, utils, withr Suggests: BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 734094bec5e65b0bcc54ae966f188a6a Package: shinyepico Version: 1.17.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE MD5sum: f09f759aa8515f7410cafc05f1d0d8c3 Package: shinyMethyl Version: 1.45.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 4213d753d51a4b5bcb923cb8acb96249 Package: ShortRead Version: 1.67.1 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Seqinfo, GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: 74c2d064380eda9efd990523e445485f Package: SIAMCAT Version: 2.13.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: 9e4d74bed2b743af10d4494b0b1ffaf9 Package: SICtools Version: 1.39.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e483eb57cc71dc6508db5d91eb8a5e59 Package: SigCheck Version: 2.41.0 Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: 5b0d895ddc2f25597a03c6137bd76be4 Package: sigFeature Version: 1.27.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) MD5sum: f3438a89a9b5c14ce2dfd2969dd6f3a2 Package: siggenes Version: 1.83.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 9b18020348d7381f31b0cf9127326a74 Package: sights Version: 1.35.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 5ce81c2ff8a387276ae3586407d4340e Package: signatureSearch Version: 1.23.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: f06e1bbaf5198687535207ac39c10fe2 Package: signeR Version: 2.11.2 Depends: R (>= 4.1.0), NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome, broom, VariantAnnotation LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: 629c11884156b25fdad02388152039d4 Package: signifinder Version: 1.11.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats, scales, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 27751cbbf5b7a66c2a3726d9fee67412 Package: SigsPack Version: 1.23.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 70de6df0dd23896647e35ec36b4051b2 Package: sigsquared Version: 1.41.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: c1fbf16e7a847555a88e1a224d8b3ef0 Package: SIM Version: 1.79.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: af5c08f5bbec4079306a67f4c14a9a9f Package: SIMAT Version: 1.41.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 97b9cce8d6880b583507a4f2414e9ea1 Package: SimBu Version: 1.11.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: ad236c51a81e9aafdc437b4f3c0c1164 Package: SIMD Version: 1.27.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: 1911a51d17d435dc075747df4d4033e7 Package: SimFFPE Version: 1.21.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: dcd90f8e22a49a165e07c6bbb54ffb99 Package: similaRpeak Version: 1.41.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 91b7d625765d9c89fd91b030a86be2df Package: SIMLR Version: 1.35.1 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: 9067c733212d4badae6769138d186a69 Package: simona Version: 1.7.1 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny, fastmatch LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: 8c9e24de6cf6cb9ced70e7cf547d8039 Package: simPIC Version: 1.5.3 Depends: R (>= 4.5.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick License: GPL-3 MD5sum: 810b88076e12e316e4b9fb33f640c1d2 Package: simpleSeg Version: 1.11.1 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: bb5343da2cff66c2a5c5a0c498ee66b6 Package: simplifyEnrichment Version: 2.3.0 Depends: R (>= 4.1.0) Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: 8d2df496199e5319446bde6e8fbfcb11 Package: sincell Version: 1.41.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 61262faa6cc9ace4c1c4ffe9edf93f60 Package: SingleCellAlleleExperiment Version: 1.5.1 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: f98decacb014623bb9a0ba288aff1404 Package: SingleCellExperiment Version: 1.31.1 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 7779307ce94a21133bff11bee4f2e208 Package: SingleCellSignalR Version: 1.99.1 Depends: R (>= 4.5) Imports: stats, utils, methods, ggplot2, matrixTests, matrixStats, foreach, BulkSignalR Suggests: knitr, markdown, rmarkdown License: CeCILL | file LICENSE MD5sum: 31af29dd89d6fc9629dedea5fafdf500 Package: SingleMoleculeFootprinting Version: 2.3.2 Depends: R (>= 4.4.0) Imports: BiocGenerics, Biostrings, BSgenome, cluster, dplyr, Seqinfo, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, magrittr, Matrix, methods, miscTools, parallel, parallelDist, patchwork, plyranges, qs, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, utils, viridis Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, rrapply, SingleMoleculeFootprintingData, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: a2235ec3073858ad1faf51bc16f9fae4 Package: SingleR Version: 2.11.3 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>= 2.25.1) LinkingTo: Rcpp, beachmat, assorthead (>= 1.3.5), BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scrapper, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: 7afc93797f521f172d72af92514dc386 Package: SiPSiC Version: 1.9.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: cfb06a7c05d8098d525935d78d448516 Package: sitadela Version: 1.17.1 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, Seqinfo, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: GenomeInfoDb, BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: 1c75b917693ea7e7b3feacb11d95cb79 Package: Site2Target Version: 1.1.0 Depends: R (>= 4.4) Imports: S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS, IRanges, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: 20ca10fd51d8b4f1c3957e34f706aab6 Package: sitePath Version: 1.25.1 Depends: R (>= 4.2) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: eba1ed825a3af81d1c5f1dfdaccfd658 Package: sizepower Version: 1.79.0 Depends: stats License: LGPL MD5sum: 0bab21424eba6ea77fad996813ef9b4c Package: sketchR Version: 1.5.2 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment, snifter, uwot, bluster, class License: MIT + file LICENSE MD5sum: 86ee3a75a639f2d7cbfd0d0f2fdf3d68 Package: skewr Version: 1.41.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: c7e33617fb2de3ee390c3bb18628f7c6 Package: slingshot Version: 2.17.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 584e5c8c9c62586d898303affe2d99f8 Package: SLqPCR Version: 1.75.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: 91b13f474967f249906372d2cc70dee4 Package: SMAD Version: 1.25.0 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 71ecdd7c8e939583e557757a07750dae Package: smartid Version: 1.5.0 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: 38e0413777916466eeeef09f5d10b455 Package: SMITE Version: 1.37.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 7415f5e32253ebda1fbc82648372e9a5 Package: smoothclust Version: 1.5.7 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, Matrix, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: 974886dc9b0f6ada0927de95fbe21ca1 Package: smoppix Version: 1.1.9 Depends: R (>= 4.4.0) Imports: spatstat.geom(>= 3.2.0),spatstat.random,methods,BiocParallel,SummarizedExperiment,SpatialExperiment,scam,Rdpack,stats,utils,extraDistr,lmerTest,lme4,ggplot2,graphics,grDevices,Rcpp (>= 1.0.11),spatstat.model,openxlsx,Rfast LinkingTo: Rcpp Suggests: testthat,rmarkdown,knitr,DropletUtils,polyCub,RImageJROI,sp,ape,htmltools,funkycells,glmnet,doParallel License: GPL-2 MD5sum: 0cb4a4868a957e0e1f2faa0f300d263b Package: SNAGEE Version: 1.49.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: c98975b596cbabe6d5ed36e3aed284cc Package: snapcount Version: 1.21.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: dff2dd10336b7a6673672ffd89af7e2b Package: snifter Version: 1.19.3 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 20a0c5c873c3b065b1a86b556b065db0 Package: snm Version: 1.57.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: ed4358f2a142af410faa666a96ab39bc Package: SNPediaR Version: 1.35.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: e2df06dc66057508e57b6d5dc1fdea34 Package: SNPhood Version: 1.39.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8), BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) MD5sum: ded5b9ab530519149aac6f8abe106ab3 Package: SNPRelate Version: 1.43.1 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods, RhpcBLASctl LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: 3d0268a9ce3c1e14617aab7f01669e3a Package: snpStats Version: 1.59.2 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics Suggests: hexbin License: GPL-3 MD5sum: 300db580f200274bead135298166ce7f Package: sosta Version: 1.1.1 Depends: R (>= 4.4.0) Imports: terra, sf, smoothr, spatstat.explore, spatstat.geom, SpatialExperiment, SingleCellExperiment, dplyr, ggplot2, patchwork, SummarizedExperiment, stats, rlang, parallel, EBImage, spatstat.random, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest, ggfortify, tidyr, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: b2cf3ce7432771fab3a662a5eccf9572 Package: SpaceTrooper Version: 0.99.43 Depends: R (>= 4.4.0), SpatialExperiment Imports: DropletUtils, S4Vectors, SummarizedExperiment, arrow, data.table, dplyr, e1071, ggplot2, ggpubr, robustbase, scater, scuttle, sf, sfheaders, tmap, cowplot, glmnet, rhdf5, methods, rlang, SpatialExperimentIO Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), withr, viridis License: MIT + file LICENSE MD5sum: 3424521b510d435f4d1369a0f55f0d1b Package: spacexr Version: 1.1.1 Depends: R (>= 4.5.0) Imports: ggplot2, Matrix, parallel, quadprog, httr, methods, memoise, BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie, SpatialExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) MD5sum: 34204d836eca0280b3879e3a0166aff3 Package: Spaniel Version: 1.23.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, 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reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: 442d7e5c65f94bf6fe4294b6b8fc03b9 Package: SpatialOmicsOverlay Version: 1.9.2 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 2e43cc74dd459ff7da3f06bed27e9665 Package: spatialSimGP Version: 1.3.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: 782dd771c0485c2df9dba34ed8336843 Package: speckle Version: 1.9.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 884def12bda5f1a8667d3f4178070db0 Package: specL Version: 1.43.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit 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covr License: MIT + file LICENSE MD5sum: fb94150bfbb800b0d5f3578974c3c777 Package: SpectraQL Version: 1.3.1 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR License: Artistic-2.0 MD5sum: 53657b632f71bee8a30b6b46803ae746 Package: SPEM Version: 1.49.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: 2f96ef3321acd15fe498d0d0fdf85732 Package: SPIA Version: 2.61.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: 624c340db9132ce272150e8036d91a09 Package: SPIAT Version: 1.11.0 Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0) Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 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lifecycle, lmerTest, magrittr, methods, pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore, spatstat.geom, stats, survival, tibble, tidyr Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: bb2f324ac7e01347175130d70d0d2816 Package: spikeLI Version: 2.69.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: 1b7be2d50ad5ea0a1d334158aa80cb72 Package: spiky Version: 1.15.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: 657015bf66b1e93aed580a532287d760 Package: spillR Version: 1.5.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, 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BiocStyle, ggplot2, ggpubr, MASS, scales, scRNAseq, testthat (>= 3.0.0) License: GPL-2 MD5sum: 4d43d94e65f7b10f98db51f0ba788af4 Package: splineTimeR Version: 1.37.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: 030e4fb777e2939f1b2c239287da0ffe Package: splots Version: 1.75.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 License: LGPL MD5sum: bdedf8a570aef14b0036cbdee697ac4a Package: SPONGE Version: 1.31.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA License: GPL (>= 3) MD5sum: 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knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: e580684405547722a115d2df600e2ea3 Package: SpotSweeper Version: 1.5.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices, BiocParallel Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: b988680437272310a9ffba7b1bfa2b7b Package: spqn Version: 1.21.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 MD5sum: 5e91aff3f0f7dafc5d82ba66c2f8a8ad Package: SPsimSeq Version: 1.19.0 Depends: R (>= 4.0) Imports: stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle License: GPL-2 MD5sum: 1d9e2c805ced70190cfc4d4f35d772d1 Package: squallms Version: 1.3.0 Depends: R (>= 4.1.0) Imports: xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble, ggplot2, shiny, plotly, data.table, caret, stats, graphics, utils, keys Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6cea17048c7951bc64628ed6f2d2dba2 Package: sRACIPE Version: 2.1.1 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics, doFuture, doRNG, future, foreach LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest License: MIT + file LICENSE MD5sum: 6f61181d03d0b6b329be45f107457a4f Package: SRAdb Version: 1.71.0 Depends: RSQLite, graph, RCurl Imports: R.utils Suggests: Rgraphviz 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RUVSeq Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 72eeb57b6a73e972aeaf91392380d3fa Package: STATegRa Version: 1.45.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: 4a41228e56690a6f3c74fb26c1dafc9a Package: Statial Version: 1.11.6 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment, cluster, treekoR, edgeR Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 MD5sum: 3e3cc5f1f651d24a38945e741ecb7f92 Package: statTarget Version: 1.39.0 Depends: R (>= 3.6.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 2c272452cefad5db2abd7a421093994b Package: stepNorm Version: 1.81.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: 67aa1924c5660319f0b22f4b492a3621 Package: stJoincount Version: 1.11.0 Depends: R (>= 4.2.0) Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1a6af89d7ac1cba29479e070d51a5f54 Package: strandCheckR Version: 1.27.1 Depends: ggplot2 (>= 3.5.0), Rsamtools, S4Vectors Imports: BiocGenerics, dplyr, Seqinfo, GenomicAlignments, GenomicRanges, gridExtra, IRanges, grid, methods, reshape2, rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene, tidyselect Suggests: BiocStyle, knitr, magrittr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 595b38fd218b01962ad4f33fd90f4de2 Package: Streamer Version: 1.55.1 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: 810f72d73096c64cc16c3ed06d905cec Package: STRINGdb Version: 2.21.0 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: f237452c5a6fae3f8730c1868f19806a Package: Structstrings Version: 1.25.3 Depends: R (>= 4.0), S4Vectors (>= 0.47.2), IRanges (>= 2.23.9), Biostrings (>= 2.57.2) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: 155917f5a8f13e84a46dc4afa2ddc3ae Package: 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testthat, knitr License: MIT + file LICENSE MD5sum: bbc3c4d1e4e9a0779520dfbfa90cbb2e Package: SummarizedExperiment Version: 1.39.2 Depends: R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3), GenomicRanges (>= 1.61.4), Biobase Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.51.3), S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), Seqinfo, S4Arrays (>= 1.1.1), DelayedArray (>= 0.31.12) Suggests: GenomeInfoDb (>= 1.45.5), rhdf5, HDF5Array (>= 1.7.5), annotate, AnnotationDbi, GenomicFeatures, SparseArray, SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest License: Artistic-2.0 MD5sum: 216a5a54a8ee201e633a86a55b0a32e7 Package: Summix Version: 2.15.0 Depends: R (>= 4.3) Imports: dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8890d256f10e15458bbc416b0163e064 Package: SuperCellCyto Version: 0.99.2 Imports: SuperCell, data.table, Matrix, BiocParallel Suggests: flowCore, knitr, rmarkdown, usethis, testthat (>= 3.0.0), BiocSingular, bluster, scater, scran, Seurat, SingleCellExperiment, BiocStyle, magick, qs2 License: GPL-3 + file LICENSE MD5sum: 4b40192e8009c7d15ea92477730b17a5 Package: supersigs Version: 1.17.0 Depends: R (>= 4.1) Imports: assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation License: GPL-3 MD5sum: c78d12c17831d80b2e41794d5580ca64 Package: surfaltr Version: 1.15.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0.6), biomaRt (>= 2.46.0), protr (>= 1.6-2), seqinr (>= 4.2-5), ggplot2 (>= 3.3.2), utils (>= 2.10.1), stringr (>= 1.4.0), Biostrings (>= 2.58.0),readr (>= 1.4.0), httr (>= 1.4.2), testthat(>= 3.0.0), xml2(>= 1.3.2), msa (>= 1.22.0), methods (>= 4.0.3) 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clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: 714c049219f133d190fd58c09f5dbe93 Package: survtype Version: 1.25.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 MD5sum: 95acda5dd4d82db28cc534f66c9e32f6 Package: sva Version: 3.57.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: 366ca262cb6f4172f3e2f23f8643c1a1 Package: svaNUMT Version: 1.15.1 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) Imports: assertthat, stringr, dplyr, methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb, GenomicFeatures, pwalign Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 59f632f775e797de1d847b4bf1c7061a Package: svaRetro Version: 1.15.1 Depends: GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0) Imports: VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb, GenomicFeatures, utils Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 0dba342ac244a33189bf507bcacf2f35 Package: SVMDO Version: 1.9.0 Depends: R(>= 4.4), shiny (>= 1.7.4) Imports: shinyFiles (>= 0.9.3), shinytitle (>= 0.1.0), golem (>= 0.3.5), nortest (>= 1.0-4), e1071 (>= 1.7-12), BSDA (>= 1.2.1), data.table (>= 1.14.6), sjmisc (>= 2.8.9), klaR (>= 1.7-1), caTools (>= 1.18.2), caret (>= 6.0-93), survival (>= 3.4-0), DT (>= 0.33.0), 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rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 4d8b74c5726755ff5ea949fa8d4f5aef Package: TADCompare Version: 1.19.0 Depends: R (>= 4.0) Imports: dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, SpectralTAD, magick, qpdf License: MIT + file LICENSE MD5sum: 8bb986820696ee5538719d3b30eb296a Package: tanggle Version: 1.15.2 Depends: R (>= 4.1), ggplot2 (>= 2.2.0), ggtree Imports: ape (>= 5.0), phangorn (>= 2.12), utils, methods Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown License: Artistic-2.0 MD5sum: ef8562758685274008f765e3f7534a29 Package: TAPseq Version: 1.21.0 Depends: R (>= 4.0.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle License: MIT + file LICENSE MD5sum: 5be18c744d76f045b5d709b95453c5f1 Package: target Version: 1.23.1 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: 90f7312f33dfc909341826594cd688be Package: TargetDecoy Version: 1.15.0 Depends: R (>= 4.1) Imports: ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: 4a5a174a90a48a140e42ac55491468e5 Package: TargetScore Version: 1.47.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: ad5b78872be9e3ff73315db221ad7f13 Package: TargetSearch Version: 2.11.1 Imports: graphics, grDevices, methods, ncdf4, stats, utils, assertthat Suggests: 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testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid, DT License: GPL (>= 3) MD5sum: 609be688b16fd6082f936587cef38f66 Package: TCGAutils Version: 1.29.5 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment, rvest, S4Vectors, Seqinfo, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox, rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 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GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, ggplot2, dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats Suggests: tidySummarizedExperiment, plyranges, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 08802e5a2e8f045f0193c10272b43226 Package: tidyFlowCore Version: 1.3.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang, stats, stringr, tibble, tidyr Suggests: BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c5af05c073f3af957decd5072acafd25 Package: tidyomics Version: 1.5.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang, stringr, cli, utils Suggests: tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6) License: MIT + file LICENSE MD5sum: 20ebb2995c55625ea31864e4705ca774 Package: tidysbml Version: 1.3.0 Depends: R (>= 4.4.0) Imports: xml2, methods Suggests: rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>= 3.0.0) License: CC BY 4.0 MD5sum: 5a6602c1c9c98d85fc3c40eb10baa22f Package: tidySingleCellExperiment Version: 1.19.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: dplyr, tidyr, ttservice (>= 0.4.0), SummarizedExperiment, tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, Matrix, stats Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly License: GPL-3 MD5sum: 9d945461f5a3e86458e4a43c82707852 Package: tidySpatialExperiment Version: 1.5.0 Depends: R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment Imports: ttservice, SummarizedExperiment, SingleCellExperiment, BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2, plotly, rlang, purrr, stringr, vctrs, tidyselect, pillar, cli, fansi, lifecycle, magick, tidygate (>= 1.0.13), shiny Suggests: BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment License: GPL (>= 3) MD5sum: 168a581fc7d292d7db504facfe395da7 Package: tidySummarizedExperiment Version: 1.19.0 Depends: R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0) Imports: dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, plotly License: GPL-3 MD5sum: 547d52e49764f652dd9734bdb2e8a263 Package: tigre Version: 1.63.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: 63d53d98eb396a8e8bc4329c0e84c057 Package: TileDBArray Version: 1.19.1 Depends: SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7) Imports: methods, tiledb, S4Vectors Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: ef3498b7cb401dc187afb3c7336cbb07 Package: tilingArray Version: 1.87.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: b4005f8d4ae18788c48f1dec583c5c8f Package: timecourse Version: 1.81.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: ec67fb61a9068d4b4e2aa72db7242793 Package: timeOmics Version: 1.21.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: e9f6a45e652b9cdb4f2b4fe9fcdda1d8 Package: timescape Version: 1.33.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 9a1ac34a515922b4844235af327daee8 Package: TIN Version: 1.41.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: e4ce36177f9b0d76d72dc578a2502e4b Package: TissueEnrich Version: 1.29.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 228f5e528f97e072a20ad9018b2bbcd4 Package: tkWidgets Version: 1.87.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: eeffc08fa088db906efee788547b7f72 Package: tLOH Version: 1.17.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 95bf73a987866653d6fa8beb76196453 Package: TMixClust Version: 1.31.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) MD5sum: 7985e7a971d1ab08e6923368eee053f8 Package: TMSig Version: 1.3.0 Depends: R (>= 4.4.0), limma Imports: circlize, ComplexHeatmap, data.table, grDevices, grid, GSEABase, Matrix, methods, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 644f4731a1d8d6a22405e88a77097fb0 Package: TnT Version: 1.31.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: 556c455c3c368f51366b75c28344d21a Package: TOAST Version: 1.23.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 MD5sum: 5f0a210d4d5f57628ec24692f2ce7ebd Package: tomoda Version: 1.19.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 1b598e296e372aa40e218402c7645196 Package: tomoseqr Version: 1.13.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 094459852af894243b55b627f1ac3e25 Package: TOP Version: 1.9.0 Depends: R (>= 4.1.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: a9459eabc7a86f63bad36ac4f67b3b4c Package: topconfects Version: 1.25.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2, scales, grid, grDevices Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: 4f9356a66389a1b21279e675c9e29a28 Package: topdownr Version: 1.31.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: 11c2eebb3d2fc77b1f12a6a6ff26ee0b Package: topGO Version: 2.61.1 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, multtest, Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown License: LGPL MD5sum: 6f722c15d6a48eb3fb6624e88eb204a8 Package: ToxicoGx Version: 2.13.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: 2186ae7fb51fa731e9ecfbfdba018a3c Package: TPP Version: 3.37.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: a5c3c13e6f7654ef286970c69f9ea4e0 Package: TPP2D Version: 1.25.2 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: 07d7f69c0eae24fdde80ab93df40205a Package: tpSVG Version: 1.5.0 Depends: mgcv, R (>= 4.4) Imports: stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: d79499bff2b5732dc23f2929854f3171 Package: tracktables Version: 1.43.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 0407939b48239c6e1ec7d798062b220e Package: trackViewer Version: 1.45.2 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: d0ec97a0ea60ced03d3d5c83575c3577 Package: tradeSeq Version: 1.23.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats License: MIT + file LICENSE MD5sum: a40346bb330e61d829cd4351eb734a7e Package: TrajectoryGeometry Version: 1.17.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: 1b9c0d48b45bddc3054a3330ddf3086c Package: TrajectoryUtils Version: 1.17.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 8ecfa99ef2060300d9f23de7074203ed Package: transcriptogramer Version: 1.31.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: bd2cb6d984897e43f95075621afba1dd Package: transcriptR Version: 1.37.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: 813195fe4b9a05c7ae2ceded9cbf5ef6 Package: transformGamPoi Version: 1.15.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: d4d5137e908ce307b67854d0768947e2 Package: transite Version: 1.27.1 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), stringr (>= 1.5.1), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 751b6db0329bfe2047328a22b6ded412 Package: tRanslatome Version: 1.47.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 8965dfc358d36decd5656dc204ada01d Package: transmogR Version: 1.5.2 Depends: R (>= 4.1.0), Biostrings, GenomicRanges Imports: BSgenome, data.table, Seqinfo, GenomicFeatures, ggplot2 (>= 4.0.0), IRanges, jsonlite, matrixStats, methods, parallel, patchwork, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, edgeR, extraChIPs, InteractionSet, knitr, readr, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0) License: GPL-3 MD5sum: 784658f1f57cd9c0c762e116459cd642 Package: transomics2cytoscape Version: 1.19.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 8d525d362ba43ee5762b61a3e34e1766 Package: TransView Version: 1.53.1 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, gplots LinkingTo: Rhtslib (>= 1.99.1) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: dcb409ff11c2b93e2918562465f3cce5 Package: traseR Version: 1.39.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: d7851b30957715288d0b00f39a7956fd Package: TreeAndLeaf Version: 1.21.0 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: a56e9e0a6bb1254786734735e32d8a94 Package: treeclimbR Version: 1.5.1 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle, GenomeInfoDb License: Artistic-2.0 MD5sum: 4fafe91b6e1a7e16348dbf0494c71930 Package: treeio Version: 1.33.0 Depends: R (>= 4.1.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: efbd744c0d986f3ca62070a646e1bb2f Package: treekoR Version: 1.17.0 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: 863f69de19a3b2da493464767b538afc Package: TreeSummarizedExperiment Version: 2.17.1 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 83c291d2fb9ee2f1c7d4466fc5b22ea3 Package: TREG Version: 1.13.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: 413326be8e12fe26dfa95d9a02564ddd Package: Trendy Version: 1.31.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 04b35bfbe0b36e5a861c77f69210c617 Package: TRESS Version: 1.15.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: fb2305fba2bc646535e1e1263403161f Package: tricycle Version: 1.17.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 83476e361fc88afc5c4fef13c545953f Package: TrIdent Version: 1.1.4 Depends: R (>= 4.2.0) Imports: graphics, utils, stats, dplyr, ggplot2, patchwork, stringr, tidyr, roll Suggests: BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0) License: GPL-2 MD5sum: 60aa1dc37ab582c92fce167cfd30e514 Package: trio Version: 3.47.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1), data.table Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: acebc8ccd9ad17e7778ede5681969786 Package: triplex Version: 1.49.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 34ecd55ca59269f2194f557c318409ac Package: tripr Version: 1.15.0 Depends: R (>= 4.1.0), shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: ae9895f48e3477ee3ed103d9eaf2300f Package: tRNA Version: 1.27.1 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: a43e2ead66deba7159426ef08bda5d84 Package: tRNAdbImport Version: 1.27.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 43d21c7b97a734131d7bb08658177813 Package: tRNAscanImport Version: 1.29.1 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, Seqinfo, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 4d9de8dab2caf8c4cb6a2583ef60e05b Package: TRONCO Version: 2.41.1 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: 4a0983eff772e2a140e632fa246814c9 Package: TSAR Version: 1.7.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 919bcec3a39538ded455781cd7bae511 Package: TSCAN Version: 1.47.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: f3821efef36570172ba5866fb252f480 Package: ttgsea Version: 1.17.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 6550d9f0deac3adf7536ee0abbbfd1b9 Package: TTMap Version: 1.31.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: a9c67994aa2e5c085b750fd04b479e82 Package: TurboNorm Version: 1.57.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: 599c471307c2e89dd4bf68eb021966e4 Package: TVTB Version: 1.35.2 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, Seqinfo, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 17342172e70f63091bd18b7c6fe8767d Package: tweeDEseq Version: 1.55.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 52cd4c307952bfb3d64a518a4fb46fa2 Package: twilight Version: 1.85.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, splines, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 0d7c63738bb6266e5c45445f7e6ae52c Package: twoddpcr Version: 1.33.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: eead9c69350731e5e9e44ffbb32869c7 Package: txcutr Version: 1.15.2 Depends: R (>= 4.5.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3, GenomeInfoDbData License: GPL-3 MD5sum: f29a09ddeb2eba7b390a60d5cbb5bef3 Package: txdbmaker Version: 1.5.6 Depends: BiocGenerics, S4Vectors, Seqinfo, GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4) Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, GenomeInfoDb, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, ensembldb, GenomeInfoDbData, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 2838131a6218d53efb034f31963cdb5d Package: tximeta Version: 1.27.15 Depends: R (>= 4.1.0) Imports: SummarizedExperiment (>= 1.39.1), tximport, jsonlite, S4Vectors, IRanges, GenomicRanges (>= 1.61.1), AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, Seqinfo, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData (>= 1.37.5), org.Dm.eg.db, DESeq2, edgeR, limma, devtools, macrophage License: GPL-2 MD5sum: 6d18e90b794c230f51195e3b59e4faf5 Package: tximport Version: 1.37.2 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: 1295bf724d1beaa7ee7b97e72b109027 Package: UCell Version: 2.13.3 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 784d053e08e8a001c814da767029b943 Package: UCSC.utils Version: 1.5.0 Imports: methods, stats, httr, jsonlite, S4Vectors Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4beb12708e919dcdf3f859ab0bab0c64 Package: Ularcirc Version: 1.27.2 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, moments, Organism.dplyr, plotgardener,R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 24405c6621b5d61a0c7f61771c6be074 Package: UMI4Cats Version: 1.19.2 Depends: R (>= 4.1.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: d7a6871ea9729b604b646a46edb42793 Package: uncoverappLib Version: 1.19.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: f86ad531ea3ac4cb296b487e2221d7db Package: UNDO Version: 1.51.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 2e84fa5d3c357fde3dacca98e1fc90f0 Package: unifiedWMWqPCR Version: 1.45.0 Depends: methods Imports: BiocGenerics, limma, stats, graphics License: GPL (>= 2) MD5sum: f04b6d762b5304e47970ceade706c697 Package: UniProt.ws Version: 2.49.4 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, BiocGenerics, httr2, jsonlite, methods, progress, rjsoncons, rlang, utils Suggests: BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: af5dfc4c527aa83995b5309921d3a580 Package: Uniquorn Version: 2.29.1 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table, GenomeInfoDb Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 MD5sum: b41012c323a6bbae38b81449f5289924 Package: universalmotif Version: 1.27.4 Depends: R (>= 4.1.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 63328fe0b783f5d920a6a1f8d4a35f9a Package: updateObject Version: 1.13.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d6c58f9f2f4f9a7535260c1e2acaf29a Package: UPDhmm Version: 1.5.0 Depends: R (>= 4.3.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr License: MIT + file LICENSE MD5sum: ebf204bf3fb37d2b5152baee665fa9a7 Package: uSORT Version: 1.35.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: 1ba1312d8b1fd3b6f9235455c677ea34 Package: VAExprs Version: 1.15.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: f63b97de565bf3d290fc60fcef6ca742 Package: VanillaICE Version: 1.71.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 6ae75d0106d12358b2532a74dd68c0ee Package: VarCon Version: 1.17.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: fcfea7a6c269d7f5779e0449c6e8d137 Package: variancePartition Version: 1.39.3 Depends: R (>= 4.3.0), ggplot2, limma (>= 3.62.2), BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: d1db5b8761ca43c2622c3848261640ed Package: VariantAnnotation Version: 1.55.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1) Imports: utils, DBI, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1), BSgenome (>= 1.77.1), GenomicFeatures (>= 1.61.4) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: GenomeInfoDb, RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: 994bf769805d048d51469a9dc82b0771 Package: VariantFiltering Version: 1.45.2 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), Biostrings (>= 2.77.2), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), GenomicFeatures (>= 1.61.4), Rsamtools (>= 2.25.1), BSgenome (>= 1.77.1), GenomicScores (>= 2.21.4), Gviz (>= 1.53.1), shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 4f522307dc3b75e6186912143d3f1285 Package: VaSP Version: 1.21.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 037f4bc50b7d0e8861996c38775fdcd3 Package: vbmp Version: 1.77.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 407d3a73d5207861d727e6a120f2e617 Package: VCFArray Version: 1.25.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: 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VennDetail Version: 1.25.3 Depends: R (>= 4.0.0), Imports: dplyr, DT, methods, ggplot2, grDevices, magrittr, patchwork, plotly, purrr, rlang, shiny, stats, tibble, tidyr, htmlwidgets, utils Suggests: knitr, markdown, RColorBrewer, rmarkdown, rstudioapi, testthat (>= 3.0.0) License: GPL-2 MD5sum: 0c472516e2329a9e79418e69a3ac62da Package: VERSO Version: 1.19.1 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 7b667a0dc0f9eb0b830d93d119d95a6e Package: vidger Version: 1.29.1 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: a60dbe1569240bd33a4bb6a54b8e2768 Package: viper Version: 1.43.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: 14599a1888095dc4d72b568b7f93837c Package: ViSEAGO Version: 1.23.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, dendextend, dynamicTreeCut, GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT, DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea, ggplot2, htmlwidgets, igraph, methods, plotly, scales, ComplexHeatmap, circlize Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager, stats, utils, grDevices, processx MD5sum: a255f44238b70266ec14a8e0d048f298 Package: VisiumIO Version: 1.5.8 Depends: R (>= 4.5.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, data.table, knitr, readr, rmarkdown, sf, tinytest License: Artistic-2.0 MD5sum: c19d8fd2165b65171a47f54b6c26e176 Package: visiumStitched Version: 1.1.1 Depends: R (>= 4.4), SpatialExperiment Imports: BiocBaseUtils, BiocGenerics, clue, dplyr, DropletUtils, grDevices, imager, Matrix, methods, pkgcond, readr, rjson, S4Vectors, SingleCellExperiment, spatialLIBD (>= 1.17.8), stringr, SummarizedExperiment, tibble, tidyr, xml2 Suggests: BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR, rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: ae0e6fb3fc0d6f51cde05de6f4aa8097 Package: vissE Version: 1.17.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: 153d6a5a78b55779a90f140fe3f18f73 Package: vmrseq Version: 1.1.2 Depends: R (>= 4.5.0) Imports: bumphunter, dplyr, BiocParallel, DelayedArray, GenomicRanges, ggplot2, methods, tidyr, locfit, gamlss.dist, recommenderlab, HDF5Array, data.table, SummarizedExperiment, IRanges, S4Vectors, devtools Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 354fce6bfd85734802f3f92cc731715b Package: Voyager Version: 1.11.0 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 438d8c7b63990144c4607026e7902488 Package: VplotR Version: 1.19.1 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, Seqinfo, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: 83c4ab46da90bde85762d36b939afe06 Package: vsclust Version: 1.11.2 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, clusterProfiler, DOSE, httr, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr License: GPL-2 MD5sum: 02dcfdc3bc55d9f1f0bb7d507f2286d6 Package: vsn Version: 3.77.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: 8fb51d4226acc7638dba944dd79f6aa2 Package: vtpnet Version: 0.49.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 03ddb1e3c904b906272a6541ee83faed Package: vulcan Version: 1.31.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: 2b9b66e6ac39d8acbe046eceb51174b6 Package: wateRmelon Version: 2.15.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: 6f602699df7e2131b4c68e5b6711a7ba Package: wavClusteR Version: 2.43.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: fe0820f8717f2a18ed6217eb973b3d5f Package: weaver Version: 1.75.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: f2c886700b299bf3d02a7bf118a38716 Package: webbioc Version: 1.81.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: a15f4621e9c314292c1d992416b6ba64 Package: weitrix Version: 1.21.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: 5ffbd6a47fe1e7b2a83f7eb9dfa4e5d4 Package: widgetTools Version: 1.87.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 87f0777ae6fe8bd21b18ae41a93c4fe2 Package: wpm Version: 1.19.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 02e00d8bbf33092fb3a178a01ff7d496 Package: Wrench Version: 1.27.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 76434a783035108c22d19c08946df7cd Package: XAItest Version: 1.1.5 Depends: R (>= 3.5.0) Imports: limma, randomForest, kernelshap, caret, lime, DT, methods, SummarizedExperiment, ggplot2 Suggests: knitr, ggforce, shapr (>= 1.0.1), airway, xgboost, BiocGenerics, RUnit, S4Vectors License: MIT + file LICENSE MD5sum: 367c38050d775de3c78b63c5ce1d2ca9 Package: xcms Version: 4.7.2 Depends: R (>= 4.1.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.37.1), lattice, MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures, MsExperiment (>= 1.5.4), Spectra (>= 1.16.1), progress, RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv, rhdf5 Enhances: Rgraphviz, rgl License: GPL (>= 2) + file LICENSE MD5sum: 4295a69e70b6f8dd5d9c252852ad3904 Package: xcore Version: 1.13.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 MD5sum: 998501d6279b69ab8d70d5ffa6be95cb Package: XDE Version: 2.55.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: d36ca97bd1d15f3015ae216cffeb9c74 Package: XeniumIO Version: 1.1.3 Depends: TENxIO, R (>= 4.5.0) Imports: BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, VisiumIO Suggests: arrow, BiocFileCache, BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 1f8df07337e4bca73daf3dce9b2c2226 Package: xenLite Version: 1.3.0 Depends: R (>= 4.1) Imports: SpatialExperiment, BiocFileCache, Matrix, S4Vectors, SummarizedExperiment, methods, utils, EBImage, shiny, HDF5Array, arrow, ggplot2, SingleCellExperiment, TENxIO, dplyr, graphics, stats Suggests: knitr, testthat, BiocStyle, yesno, terra, SpatialFeatureExperiment, SFEData, tiff License: Artistic-2.0 MD5sum: 0996340bf5229666a6b5f91315ee4e53 Package: Xeva Version: 1.25.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 2bde2138ebbc493dfbedd7283786374d Package: XINA Version: 1.27.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 051203f16055ad7a2bb142c6fcc75153 Package: xmapbridge Version: 1.67.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 468f7bc34efec17aa97ab5007f4ab19f Package: XVector Version: 0.49.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9) Imports: methods, utils, tools, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: f7a348596f8e279a3e825705b0704fce Package: yamss Version: 1.35.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: 9747695eae2389d4489f390382dc6ec4 Package: YAPSA Version: 1.35.1 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, Seqinfo, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 3c4165ab97953fbf170fc117403bac5f Package: yarn Version: 1.35.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: 954802ed3a411fe9b83aff2cdb8cf5b4 Package: zellkonverter Version: 1.19.2 Imports: basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment (>= 1.11.6), SparseArray, SummarizedExperiment, utils Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, SpatialExperiment, spelling, testthat, withr License: MIT + file LICENSE MD5sum: 76d2900e06cd0df48016c8138ac1478a Package: zenith Version: 1.11.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr, Rfast, ggplot2, tidyr, dplyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: 800099c881b2cff5ec27615c64d1389b Package: zFPKM Version: 1.31.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: ad19c5ff08e7b38bf03b45622b6aaa43 Package: zinbwave Version: 1.31.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 MD5sum: f0ecc512ecb23a49717d0310069418de Package: zitools Version: 1.3.0 Depends: R (>= 4.4.0), methods Imports: phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment, stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2, reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome License: BSD_3_clause + file LICENSE MD5sum: fd9fa1354cc0728c877026cdea54fb82 Package: ZygosityPredictor Version: 1.9.1 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang Suggests: rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 01d99d7e7613370365d9e45a1b18650a