methylGSA

Gene Set Analysis Using the Outcome of Differential Methylation

Bioconductor version: 3.24 · Package version: 1.31.0

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.

Installation

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

BiocManager::install("methylGSA")

Details

Maintainer	Xu Ren <xuren2120@gmail.com>
Author	Xu Ren [aut, cre], Pei Fen Kuan [aut]
License	GPL-2
URL	https://github.com/reese3928/methylGSA
Bug Reports	https://github.com/reese3928/methylGSA/issues
Downloads rank	594
Source branch	devel
biocViews	DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software

Documentation

methylGSA: Gene Set Analysis for DNA Methylation Datasets

Download

Follow the installation instructions to use this package in your R session.

Source package	methylGSA_1.31.0.tar.gz
Windows binary (x86_64)	methylGSA_1.31.0.zip
macOS binary (arm64)	methylGSA_1.31.0.tgz
macOS binary (x86_64)	methylGSA_1.31.0.tgz

Dependencies

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

Suggests: knitr, rmarkdown, testthat, enrichplot