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methylGSA

Gene Set Analysis Using the Outcome of Differential Methylation


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("methylGSA")

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("methylGSA")
methylGSA: Gene Set Analysis for DNA Methylation Datasets HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software
Version 1.20.0
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
See More
Suggests knitr, rmarkdown, testthat, enrichplot
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Package Archives

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

Source Package methylGSA_1.20.0.tar.gz
Windows Binary methylGSA_1.20.0.zip
macOS Binary (x86_64) methylGSA_1.20.0.tgz
macOS Binary (arm64) methylGSA_1.20.0.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/
Package Downloads Report Download Stats