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This is the development version of methylGSA; for the stable release version, see methylGSA.

Gene Set Analysis Using the Outcome of Differential Methylation

Bioconductor version: Development (3.19)

The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.

Author: Xu Ren [aut, cre], Pei Fen Kuan [aut]

Maintainer: Xu Ren <xuren2120 at gmail.com>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

methylGSA: Gene Set Analysis for DNA Methylation Datasets HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software
Version 1.21.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Depends R (>= 3.5)
Imports RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
System Requirements
URL https://github.com/reese3928/methylGSA
Bug Reports https://github.com/reese3928/methylGSA/issues
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Suggests knitr, rmarkdown, testthat, enrichplot
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Follow Installation instructions to use this package in your R session.

Source Package methylGSA_1.21.0.tar.gz
Windows Binary methylGSA_1.21.0.zip
macOS Binary (x86_64) methylGSA_1.21.0.tgz
macOS Binary (arm64) methylGSA_1.21.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/methylGSA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methylGSA
Bioc Package Browser https://code.bioconductor.org/browse/methylGSA/
Package Short Url https://bioconductor.org/packages/methylGSA/
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