methylGSA

DOI: 10.18129/B9.bioc.methylGSA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see methylGSA.

Gene Set Analysis Using the Outcome of Differential Methylation

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software
Version	1.2.3
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	GPL-2
Depends	R (>= 3.5)
Imports	RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19
LinkingTo
Suggests	knitr, rmarkdown, testthat, enrichplot
SystemRequirements
Enhances
URL	https://github.com/reese3928/methylGSA
BugReports	https://github.com/reese3928/methylGSA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	methylGSA_1.2.3.tar.gz
Windows Binary	methylGSA_1.2.3.zip
Mac OS X 10.11 (El Capitan)	methylGSA_1.2.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylGSA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylGSA
Package Short Url	https://bioconductor.org/packages/methylGSA/
Package Downloads Report	Download Stats