escape

DOI: 10.18129/B9.bioc.escape    

Easy single cell analysis platform for enrichment

Bioconductor version: Release (3.13)

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 GSEA across individual cells.

Author: Nick Borcherding [aut, cre], Jared Andrews [aut]

Maintainer: Nick Borcherding <ncborch at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Escape-ingToWork
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	Apache License 2.0
Depends	R (>= 4.0)
Imports	grDevices, dplyr, ggplot2, GSEABase, GSVA, SingleCellExperiment, limma, ggridges, msigdbr, stats, BiocParallel, Matrix
LinkingTo
Suggests	Seurat, SeuratObject, knitr, rmarkdown, BiocStyle, testthat, dittoSeq(>= 1.1.2)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	escape_1.2.0.tar.gz
Windows Binary	escape_1.2.0.zip
macOS 10.13 (High Sierra)	escape_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/escape
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/escape
Package Short Url	https://bioconductor.org/packages/escape/
Package Downloads Report	Download Stats