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escape

Easy single cell analysis platform for enrichment


Bioconductor version: Release (3.19)

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]

Maintainer: Nick Borcherding <ncborch at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software
Version 2.0.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject
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
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Package Archives

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

Source Package escape_2.0.0.tar.gz
Windows Binary escape_2.0.0.zip
macOS Binary (x86_64) escape_2.0.0.tgz
macOS Binary (arm64) escape_2.0.0.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/
Package Downloads Report Download Stats