escape

DOI: 10.18129/B9.bioc.escape    

Easy single cell analysis platform for enrichment

Bioconductor version: Release (3.12)

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 "4.0") 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 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License Apache License 2.0
Depends R (>= 4.0)
Imports grDevices, rlang, dplyr, factoextra, ggplot2, ggrepel, GSEABase, GSVA, SingleCellExperiment, limma, ggridges, msigdbr, stats, BiocParallel
LinkingTo
Suggests Seurat, 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_1.0.0.tar.gz
Windows Binary escape_1.0.0.zip (64-bit only)
macOS 10.13 (High Sierra) escape_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/escape
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/escape
Package Short Url https://bioconductor.org/packages/escape/
Package Downloads Report Download Stats

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