escape

DOI: 10.18129/B9.bioc.escape  

Easy single cell analysis platform for enrichment

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

HTML	R Script	Escape-ingToWork
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Classification, GeneSetEnrichment, GeneSignaling, Pathways, Sequencing, SingleCell, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-2
Depends	R (>= 4.1)
Imports	grDevices, dplyr, ggplot2, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, BiocParallel, Matrix, UCell, broom, reshape2, patchwork, MatrixGenerics, utils, rlang, stringr, data.table, SummarizedExperiment, methods
LinkingTo
Suggests	Seurat, SeuratObject, knitr, rmarkdown, markdown, BiocStyle, testthat, dittoSeq(>= 1.1.2)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	Cepo
Links To Me
Build Report

Package Archives

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

Source Package	escape_1.8.0.tar.gz
Windows Binary	escape_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	escape_1.8.0.tgz
macOS Binary (arm64)	escape_1.8.0.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