ReactomePA: Reactome Pathway Analysis

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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 <guangchuangyu@gmail.com> with contributions from Vladislav Petyuk
Date of publication
None
Maintainer
Guangchuang Yu <guangchuangyu@gmail.com>
License
GPL-2
Version
1.18.1
URLs

View on Bioconductor

Man pages

DataSet
Datasets sample contains a sample of gene IDs.
enrichPathway
Pathway Enrichment Analysis of a gene set. Given a vector of...
getALLEG
getALLEG
getDb
getDb
gsePathway
gsePathway
ReactomePA-package
Reactome Pathway Analysis
viewPathway
viewPathway

Files in this package

ReactomePA/DESCRIPTION
ReactomePA/NAMESPACE
ReactomePA/NEWS
ReactomePA/R
ReactomePA/R/ReactomePA-package.R
ReactomePA/R/enrichPathway.R
ReactomePA/R/gseAnalyzer.R
ReactomePA/R/utilities.R
ReactomePA/R/viewPathway.R
ReactomePA/R/zzz.R
ReactomePA/README.md
ReactomePA/build
ReactomePA/build/vignette.rds
ReactomePA/inst
ReactomePA/inst/CITATION
ReactomePA/inst/doc
ReactomePA/inst/doc/ReactomePA.R
ReactomePA/inst/doc/ReactomePA.Rmd
ReactomePA/inst/doc/ReactomePA.html
ReactomePA/man
ReactomePA/man/DataSet.Rd
ReactomePA/man/ReactomePA-package.Rd
ReactomePA/man/enrichPathway.Rd
ReactomePA/man/getALLEG.Rd
ReactomePA/man/getDb.Rd
ReactomePA/man/gsePathway.Rd
ReactomePA/man/viewPathway.Rd
ReactomePA/tests
ReactomePA/tests/testthat
ReactomePA/tests/testthat.R
ReactomePA/tests/testthat/test-getDb.R
ReactomePA/vignettes
ReactomePA/vignettes/ReactomePA.Rmd
ReactomePA/vignettes/ReactomePA.bib
ReactomePA/vignettes/figures
ReactomePA/vignettes/figures/E2F.png
ReactomePA/vignettes/figures/clusterProfiler.png
ReactomePA/vignettes/figures/cnetplot.png
ReactomePA/vignettes/figures/enrichMap.png
ReactomePA/vignettes/figures/enrichMap_gsea.png
ReactomePA/vignettes/nature.csl