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ReactomePA

Reactome Pathway Analysis


Bioconductor version: Release (3.19)

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.

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

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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")
An R package for Reactome Pathway Analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization
Version 1.48.0
In Bioconductor since BioC 2.10 (R-2.15) (12 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, gson
System Requirements
URL https://yulab-smu.top/biomedical-knowledge-mining-book/
Bug Reports https://github.com/GuangchuangYu/ReactomePA/issues
See More
Suggests BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat
Linking To
Enhances
Depends On Me maEndToEnd
Imports Me bioCancer, ExpHunterSuite, gINTomics, miRSM, miRspongeR, Pigengene, scTensor
Suggests Me CBNplot, ChIPseeker, CINdex, cola, GeDi, GRaNIE, scGPS
Links To Me
Build Report Build Report

Package Archives

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

Source Package ReactomePA_1.48.0.tar.gz
Windows Binary ReactomePA_1.48.0.zip (64-bit only)
macOS Binary (x86_64) ReactomePA_1.48.0.tgz
macOS Binary (arm64) ReactomePA_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ReactomePA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ReactomePA
Bioc Package Browser https://code.bioconductor.org/browse/ReactomePA/
Package Short Url https://bioconductor.org/packages/ReactomePA/
Package Downloads Report Download Stats