ReactomePA

This is the released version of ReactomePA; for the devel version, see ReactomePA.

Reactome Pathway Analysis

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DOI: 10.18129/B9.bioc.ReactomePA

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization

Version 1.54.0

In Bioconductor since BioC 2.10 (R-2.15) (13.5 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, gson, yulab.utils (>= 0.1.5)

System Requirements

URL https://yulab-smu.top/contribution-knowledge-mining/

Bug Reports https://github.com/GuangchuangYu/ReactomePA/issues

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

Linking To

Enhances

Depends On Me maEndToEnd

Imports Me bioCancer, miRSM, miRspongeR, mitology, scTensor, ExpHunterSuite, XYomics

Suggests Me CBNplot, ChIPseeker, cola, GRaNIE, scGPS, scGraphVerse

Links To Me

Build Report Build Report

Package Archives

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

Source Package ReactomePA_1.54.0.tar.gz

Windows Binary (x86_64) ReactomePA_1.53.0.zip (64-bit only)

macOS Binary (x86_64) ReactomePA_1.54.0.tgz

macOS Binary (arm64) ReactomePA_1.54.0.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/

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