escape

DOI: 10.18129/B9.bioc.escape    

This is the development version of escape; for the stable release version, see escape.

Easy single cell analysis platform for enrichment

Bioconductor version: Development (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>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.7.0
In Bioconductor since BioC 3.12 (R-4.0) (1.5 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_1.7.0.tar.gz
Windows Binary escape_1.7.0.zip
macOS 10.13 (High Sierra) escape_1.7.0.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

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