escape

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see escape.

Easy single cell analysis platform for enrichment


Bioconductor version: 3.14

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>

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

Installation

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

Details

biocViews Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Apache License 2.0
Depends R (>= 4.0)
Imports grDevices, dplyr, ggplot2, GSEABase, GSVA, SingleCellExperiment, limma, ggridges, msigdbr, stats, BiocParallel, Matrix
System Requirements
URL
See More
Suggests Seurat, SeuratObject, knitr, rmarkdown, BiocStyle, testthat, dittoSeq(>= 1.1.2)
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.

Source Package escape_1.4.0.tar.gz
Windows Binary escape_1.4.0.zip (64-bit only)
macOS 10.13 (High Sierra) escape_1.4.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive