chevreulProcess 0.99.24
chevreulProcessR is an open-source statistical environment which can be easily modified
to enhance its functionality via packages. chevreulProcess
is a R package available via the Bioconductor
repository
for packages. R can be installed on any operating system from
CRAN after which you can install
chevreulProcess by using the following commands in your R
session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("chevreulProcess")
The chevreulProcess package is designed for single-cell RNA
sequencing data. The functions included within this package are derived from
other packages that have implemented the infrastructure needed for RNA-seq data
processing and analysis. Packages that have been instrumental in the
development of chevreulProcess include,
Biocpkg("SummarizedExperiment") and Biocpkg("scater").
R and Bioconductor have a steep learning curve so it is critical to
learn where to ask for help. The
Bioconductor support site is the main
resource for getting help: remember to use the chevreulProcess tag and check
the older posts.
chevreulProcessThe chevreulProcess package contains functions to preprocess, cluster,
visualize, and perform other analyses on scRNA-seq data. It also contains a
shiny app for easy
visualization and analysis of scRNA data.
chvereul uses SingelCellExperiment (SCE) object type
(from SingleCellExperiment)
to store expression and other metadata from single-cell experiments.
This package features functions capable of:
library("chevreulProcess")
# Load the data
library(chevreuldata)
chevreul_sce <- human_gene_transcript_sce()
chevreul_sce
#> class: SingleCellExperiment
#> dim: 56267 794
#> metadata(4): merge.info pca.info experiment markers
#> assays(3): reconstructed counts logcounts
#> rownames(56267): 5-8S-rRNA 5S-rRNA ... ZZEF1 ZZZ3
#> rowData names(1): rotation
#> colnames(794): hs20151130-SC1-26 hs20151130-SC1-28 ...
#> 20200312-DS-dissected-81 20200312-DS-dissected-83
#> colData names(33): batch Sequencing_Run ... gene_snn_res.0.8
#> gene_snn_res.1
#> reducedDimNames(3): corrected TSNE UMAP
#> mainExpName: integrated
#> altExpNames(2): gene transcriptR session information.
#> R Under development (unstable) (2024-10-21 r87258)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] chevreuldata_0.99.25 ExperimentHub_2.15.0
#> [3] AnnotationHub_3.15.0 BiocFileCache_2.15.0
#> [5] dbplyr_2.5.0 chevreulProcess_0.99.24
#> [7] scater_1.35.0 ggplot2_3.5.1
#> [9] scuttle_1.17.0 SingleCellExperiment_1.29.1
#> [11] SummarizedExperiment_1.37.0 Biobase_2.67.0
#> [13] GenomicRanges_1.59.1 GenomeInfoDb_1.43.2
#> [15] IRanges_2.41.2 S4Vectors_0.45.2
#> [17] BiocGenerics_0.53.3 generics_0.1.3
#> [19] MatrixGenerics_1.19.1 matrixStats_1.5.0
#> [21] BiocStyle_2.35.0
#>
#> loaded via a namespace (and not attached):
#> [1] jsonlite_1.8.9 shape_1.4.6.1
#> [3] magrittr_2.0.3 ggbeeswarm_0.7.2
#> [5] GenomicFeatures_1.59.1 rmarkdown_2.29
#> [7] GlobalOptions_0.1.2 fs_1.6.5
#> [9] BiocIO_1.17.1 vctrs_0.6.5
#> [11] memoise_2.0.1 Rsamtools_2.23.1
#> [13] DelayedMatrixStats_1.29.1 RCurl_1.98-1.16
#> [15] htmltools_0.5.8.1 S4Arrays_1.7.1
#> [17] curl_6.1.0 BiocNeighbors_2.1.2
#> [19] SparseArray_1.7.2 sass_0.4.9
#> [21] bslib_0.8.0 cachem_1.1.0
#> [23] ResidualMatrix_1.17.0 GenomicAlignments_1.43.0
#> [25] igraph_2.1.3 mime_0.12
#> [27] lifecycle_1.0.4 pkgconfig_2.0.3
#> [29] rsvd_1.0.5 Matrix_1.7-1
#> [31] R6_2.5.1 fastmap_1.2.0
#> [33] GenomeInfoDbData_1.2.13 digest_0.6.37
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#> [45] bit64_4.5.2 withr_3.0.2
#> [47] BiocParallel_1.41.0 viridis_0.6.5
#> [49] DBI_1.2.3 rappdirs_0.3.3
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#> [53] bluster_1.17.0 tools_4.5.0
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#> [57] glue_1.8.0 restfulr_0.0.15
#> [59] batchelor_1.23.0 grid_4.5.0
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#> [63] gtable_0.3.6 tzdb_0.4.0
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#> [83] Biostrings_2.75.3 knitr_1.49
#> [85] gridExtra_2.3 bookdown_0.42
#> [87] ProtGenerics_1.39.1 edgeR_4.5.1
#> [89] cmdfun_1.0.2 xfun_0.50
#> [91] statmod_1.5.0 stringi_1.8.4
#> [93] UCSC.utils_1.3.0 EnsDb.Hsapiens.v86_2.99.0
#> [95] lazyeval_0.2.2 yaml_2.3.10
#> [97] evaluate_1.0.3 codetools_0.2-20
#> [99] tibble_3.2.1 BiocManager_1.30.25
#> [101] cli_3.6.3 munsell_0.5.1
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#> [107] parallel_4.5.0 readr_2.1.5
#> [109] blob_1.2.4 AnnotationFilter_1.31.0
#> [111] scran_1.35.0 sparseMatrixStats_1.19.0
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