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Bioconductor - escape

escape

This is the released version of escape; for the devel version, see escape.

Easy single cell analysis platform for enrichment

Bioconductor version: Release (3.21)

A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells.

Author: Nick Borcherding [aut, cre], Jared Andrews [aut], Alexei Martsinkovskiy [ctb]

Maintainer: Nick Borcherding <ncborch at gmail.com>

Citation (from within R, enter citation("escape")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("escape")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("escape")
Details biocViews Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software Version 2.4.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License MIT + file LICENSE Depends R (>= 4.1) Imports AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdb, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject, Matrix System Requirements URL See More Suggests Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr Linking To Enhances Depends On Me Imports Me Suggests Me Cepo Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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