methylGSA

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see methylGSA.

Gene Set Analysis Using the Outcome of Differential Methylation

Bioconductor version: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software

Version 1.26.0

In Bioconductor since BioC 3.8 (R-3.5) (7 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

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_1.26.0.tar.gz

Windows Binary (x86_64) methylGSA_1.26.0.zip

macOS Binary (x86_64) methylGSA_1.26.0.tgz

macOS Binary (arm64) methylGSA_1.26.0.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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