Package: singleCellTK
Type: Package
Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq
        Data
Version: 2.21.0
Authors@R: c(person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0003-4347-5199")),
             person(given="Irzam", family="Sarfraz", email="isarfraz@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0001-8121-792X")),
             person(given="Rui", family="Hong", email="rzhong@bu.edu", role=c("aut")),
             person(given="Yusuke", family="Koga", email="ykoga07@bu.edu", role=c("aut")),
             person(given="Salam", family="Alabdullatif", email="salamha@bu.edu", role=c("aut")),
             person(given="Nida", family="Pervaiz", email="nidapervaiz27@gmail.com", role=c("aut")),
             person(given="David", family="Jenkins", email="dfj@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0002-7451-4288")),
             person(given="Vidya", family="Akavoor", email="vidyaap@bu.edu", role=c("aut")),
             person(given="Xinyun", family="Cao", email="xcao19@bu.edu", role=c("aut")),
             person(given="Shruthi", family="Bandyadka", email="sbandya@bu.edu", role=c("aut")),
             person(given="Anastasia", family="Leshchyk", email="aleshchk@bu.edu", role=c("aut")),
             person(given="Tyler", family="Faits", email="tfaits@bu.edu", role=c("aut")),
             person(given=c("Mohammed", "Muzamil"), family="Khan", email="mmkhan@bu.edu", role=c("aut")),
             person(given="Zhe", family="Wang", email="zhe@bu.edu", role=c("aut")),
             person(given=c("W.", "Evan"), family="Johnson", email="wej@bu.edu", role=c("aut"),
                    comment = c(ORCID = "0000-0002-6247-6595")),
             person(given="Ming", family="Liu", email="mingl@bu.edu", role=c("aut")),
             person(given=c("Joshua", "David"), family="Campbell", email="camp@bu.edu", role=c("aut", "cre"),
             comment = c(ORCID = "0000-0003-0780-8662"))
             )
Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment,
        DelayedArray, Biobase
Description: The Single Cell Toolkit (SCTK) in the singleCellTK package
        provides an interface to popular tools for importing, quality
        control, analysis, and visualization of single cell RNA-seq
        data. SCTK allows users to seamlessly integrate tools from
        various packages at different stages of the analysis workflow.
        A general "a la carte" workflow gives users the ability access
        to multiple methods for data importing, calculation of general
        QC metrics, doublet detection, ambient RNA estimation and
        removal, filtering, normalization, batch correction or
        integration, dimensionality reduction, 2-D embedding,
        clustering, marker detection, differential expression, cell
        type labeling, pathway analysis, and data exporting. Curated
        workflows can be used to run Seurat and Celda. Streamlined
        quality control can be performed on the command line using the
        SCTK-QC pipeline. Users can analyze their data using commands
        in the R console or by using an interactive Shiny Graphical
        User Interface (GUI). Specific analyses or entire workflows can
        be summarized and shared with comprehensive HTML reports
        generated by Rmarkdown. Additional documentation and vignettes
        can be found at camplab.net/sctk.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: SingleCell, GeneExpression, DifferentialExpression,
        Alignment, Clustering, ImmunoOncology, BatchEffect,
        Normalization, QualityControl, DataImport, GUI
LazyData: FALSE
Imports: ape, anndata, AnnotationHub, batchelor, BiocParallel, celldex,
        colourpicker, colorspace, cowplot, cluster, ComplexHeatmap,
        data.table, DelayedMatrixStats, DESeq2, dplyr, DT,
        ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel,
        ggtree, gridExtra, grid, GSVA (>= 1.50.0), GSVAdata, igraph,
        KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats,
        methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne,
        S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>=
        3.1.3), shiny, shinyjs, SingleR, stringr, SoupX, sva, reshape2,
        shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders,
        DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools,
        tximport, tidyr, eds, withr, GSEABase, R.utils, zinbwave,
        scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr,
        scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN,
        TrajectoryUtils, scuttle, utils, stats, zellkonverter,
        lifecycle
RoxygenNote: 7.3.3
Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling,
        org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui,
        shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap
        (>= 1.1.0), harmony, SeuratObject, optparse
VignetteBuilder: knitr
URL: https://www.camplab.net/sctk/
BugReports: https://github.com/compbiomed/singleCellTK/issues
Language: en-US
Config/pak/sysreqs: libcairo2-dev libfftw3-dev libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libmagick++-dev gsfonts libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libtiff-dev libwebp-dev
        libxml2-dev libssl-dev perl python3 libnode-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:29:49 UTC
RemoteUrl: https://github.com/bioc/singleCellTK
RemoteRef: HEAD
RemoteSha: 4895b66dccfe29cc60a0bc9425e34d240df05aa3
NeedsCompilation: no
Packaged: 2025-10-30 11:31:33 UTC; root
Author: Yichen Wang [aut] (ORCID: <https://orcid.org/0000-0003-4347-5199>),
  Irzam Sarfraz [aut] (ORCID: <https://orcid.org/0000-0001-8121-792X>),
  Rui Hong [aut],
  Yusuke Koga [aut],
  Salam Alabdullatif [aut],
  Nida Pervaiz [aut],
  David Jenkins [aut] (ORCID: <https://orcid.org/0000-0002-7451-4288>),
  Vidya Akavoor [aut],
  Xinyun Cao [aut],
  Shruthi Bandyadka [aut],
  Anastasia Leshchyk [aut],
  Tyler Faits [aut],
  Mohammed Muzamil Khan [aut],
  Zhe Wang [aut],
  W. Evan Johnson [aut] (ORCID: <https://orcid.org/0000-0002-6247-6595>),
  Ming Liu [aut],
  Joshua David Campbell [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0780-8662>)
Maintainer: Joshua David Campbell <camp@bu.edu>
Built: R 4.6.0; ; 2025-10-30 11:38:21 UTC; windows
