escape

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see escape.

Easy single cell analysis platform for enrichment

Bioconductor version: 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")

Escape-ingToWork HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software

Version 2.4.0

In Bioconductor since BioC 3.12 (R-4.0) (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

Suggests Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr

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Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package escape_2.4.0.tar.gz

Windows Binary (x86_64) escape_2.4.0.zip (64-bit only)

macOS Binary (x86_64) escape_2.4.0.tgz

macOS Binary (arm64) escape_2.4.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/escape

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/escape

Bioc Package Browser https://code.bioconductor.org/browse/escape/

Package Short Url https://bioconductor.org/packages/escape/

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