ReactomePA

Reactome Pathway Analysis

Bioconductor version: 3.23 · Package version: 1.56.0

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. This package is not affiliated with the Reactome team.

Installation

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

BiocManager::install("ReactomePA")

Details

Maintainer	Guangchuang Yu <guangchuangyu@gmail.com>
Author	Guangchuang Yu [aut, cre], Vladislav Petyuk [ctb]
License	GPL-2
URL	https://yulab-smu.top/contribution-knowledge-mining/
Bug Reports	https://github.com/GuangchuangYu/ReactomePA/issues
Downloads rank	6164
Source branch	RELEASE_3_23
biocViews	Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization

Documentation

An R package for Reactome Pathway Analysis

Download

Follow the installation instructions to use this package in your R session.

Source package	ReactomePA_1.56.0.tar.gz
Windows binary (x86_64)	ReactomePA_1.56.0.zip
macOS binary (arm64)	ReactomePA_1.56.0.tgz
macOS binary (x86_64)	ReactomePA_1.56.0.tgz

Dependencies

Depends: R (>= 3.4.0)

Imports: AnnotationDbi, enrichplot, enrichit, ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite, gson, yulab.utils (>= 0.1.5)

Suggests: clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat

Reverse dependencies

Imports Me (9): bioCancer, ExpHunterSuite, famat, gINTomics, miRSM, miRspongeR, mitology, Pigengene, scTensor

Suggests Me (9): CBNplot, ChIPseeker, cola, epiSeeker, GeDi, GRaNIE, scGPS, scGraphVerse, XYomics