ReactomePA
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see ReactomePA.
Reactome Pathway Analysis
Bioconductor version: 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("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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Reactome, Software, Visualization |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12.5 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 |
| 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 | Pigengene, bioCancer, gINTomics, miRSM, miRspongeR, scTensor, ExpHunterSuite |
| Suggests Me | CBNplot, CINdex, ChIPseeker, GRaNIE, GeDi, cola, 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 (x86_64) | ReactomePA_1.48.0.zip |
| 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 |