ReactomePA

DOI: 10.18129/B9.bioc.ReactomePA    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ReactomePA.

Reactome Pathway Analysis

Bioconductor version: 3.15

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.

Author: Guangchuang Yu [aut, cre], Vladislav Petyuk [ctb]

Maintainer: Guangchuang Yu <guangchuangyu 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("ReactomePA")

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("ReactomePA")

 

HTML	R Script	An R package for Reactome Pathway Analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization
Version	1.40.0
In Bioconductor since	BioC 2.10 (R-2.15) (10.5 years)
License	GPL-2
Depends	R (>= 3.4.0)
Imports	AnnotationDbi, DOSE(>= 3.5.1), enrichplot, ggplot2 (>= 3.3.5), ggraph, reactome.db, igraph, graphite
LinkingTo
Suggests	BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat
SystemRequirements
Enhances
URL	https://yulab-smu.top/biomedical-knowledge-mining-book/
BugReports	https://github.com/GuangchuangYu/ReactomePA/issues
Depends On Me	maEndToEnd
Imports Me	bioCancer, epihet, ExpHunterSuite, miRspongeR, multiSight, Pigengene, scTensor
Suggests Me	ChIPseeker, CINdex, clusterProfiler, cola, GRaNIE, scGPS
Links To Me
Build Report

Package Archives

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

Source Package	ReactomePA_1.40.0.tar.gz
Windows Binary	ReactomePA_1.40.0.zip
macOS Binary (x86_64)	ReactomePA_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ReactomePA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ReactomePA
Package Short Url	https://bioconductor.org/packages/ReactomePA/
Package Downloads Report	Download Stats