methylGSA

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see methylGSA.

Gene Set Analysis Using the Outcome of Differential Methylation


Bioconductor version: 3.10

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 "3.6") 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 1.4.9
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package methylGSA_1.4.9.tar.gz
Windows Binary methylGSA_1.4.9.zip
Mac OS X 10.11 (El Capitan) methylGSA_1.4.9.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
Old Source Packages for BioC 3.10 Source Archive