ReactomePA
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ReactomePA.
Reactome Pathway Analysis
Bioconductor version: 3.16
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>
citation("ReactomePA")):
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")| An R package for Reactome Pathway Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization |
| Version | 1.42.0 |
| 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, epihet, ExpHunterSuite, miRspongeR, multiSight, Pigengene, scTensor |
| Suggests Me | ChIPseeker, CINdex, clusterProfiler, cola, 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_1.42.0.tar.gz |
| Windows Binary | ReactomePA_1.42.0.zip |
| macOS Binary (x86_64) | ReactomePA_1.42.0.tgz |
| macOS Binary (arm64) | ReactomePA_1.42.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |