chevreulPlot 0.99.29
chevreulPlotR is an open-source statistical environment which can be easily modified
to enhance its functionality via packages. chevreulPlot 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
chevreulPlot by using the following commands in your R session:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("chevreulPlot")
The chevreulPlot 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 chevreulPlot 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 chevreulPlot tag and check
the older posts.
chevreulPlotThe chevreulPlot 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("chevreulPlot")
# 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 transcriptsessionInfo()
#> 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_2.15.1
#> [5] dbplyr_2.5.0 chevreulPlot_0.99.29
#> [7] chevreulProcess_0.99.24 scater_1.35.0
#> [9] ggplot2_3.5.1 scuttle_1.17.0
#> [11] SingleCellExperiment_1.29.1 SummarizedExperiment_1.37.0
#> [13] Biobase_2.67.0 GenomicRanges_1.59.1
#> [15] GenomeInfoDb_1.43.2 IRanges_2.41.2
#> [17] S4Vectors_0.45.2 BiocGenerics_0.53.3
#> [19] generics_0.1.3 MatrixGenerics_1.19.1
#> [21] matrixStats_1.5.0 BiocStyle_2.35.0
#>
#> loaded via a namespace (and not attached):
#> [1] batchelor_1.23.0 BiocIO_1.17.1
#> [3] bitops_1.0-9 filelock_1.0.3
#> [5] tibble_3.2.1 XML_3.99-0.18
#> [7] lifecycle_1.0.4 edgeR_4.5.1
#> [9] doParallel_1.0.17 lattice_0.22-6
#> [11] ensembldb_2.31.0 magrittr_2.0.3
#> [13] limma_3.63.3 plotly_4.10.4
#> [15] sass_0.4.9 rmarkdown_2.29
#> [17] jquerylib_0.1.4 yaml_2.3.10
#> [19] metapod_1.15.0 DBI_1.2.3
#> [21] RColorBrewer_1.1-3 ResidualMatrix_1.17.0
#> [23] abind_1.4-8 purrr_1.0.2
#> [25] AnnotationFilter_1.31.0 RCurl_1.98-1.16
#> [27] rappdirs_0.3.3 circlize_0.4.16
#> [29] GenomeInfoDbData_1.2.13 ggrepel_0.9.6
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#> [47] GetoptLong_1.0.5 BiocNeighbors_2.1.2
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#> [51] tools_4.5.0 Rcpp_1.0.14
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#> [83] scales_1.3.0 png_0.1-8
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#> [87] tzdb_0.4.0 rjson_0.2.23
#> [89] curl_6.1.0 cachem_1.1.0
#> [91] GlobalOptions_0.1.2 stringr_1.5.1
#> [93] BiocVersion_3.21.1 parallel_4.5.0
#> [95] vipor_0.4.7 AnnotationDbi_1.69.0
#> [97] restfulr_0.0.15 pillar_1.10.1
#> [99] grid_4.5.0 vctrs_0.6.5
#> [101] BiocSingular_1.23.0 EnsDb.Hsapiens.v86_2.99.0
#> [103] beachmat_2.23.6 cluster_2.1.8
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#> [107] readr_2.1.5 GenomicFeatures_1.59.1
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#> [111] compiler_4.5.0 Rsamtools_2.23.1
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