methylGSA

DOI: 10.18129/B9.bioc.methylGSA    

Gene Set Analysis Using the Outcome of Differential Methylation

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("methylGSA", version = "3.8")

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

Details

biocViews DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software
Version 1.0.0
License GPL-2
Depends R (>= 3.5)
Imports RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, GO.db, AnnotationDbi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19
LinkingTo
Suggests knitr, rmarkdown, testthat, enrichplot
SystemRequirements
Enhances
URL https://github.com/reese3928/methylGSA
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_1.0.0.tar.gz
Windows Binary methylGSA_1.0.0.zip
Mac OS X 10.11 (El Capitan) methylGSA_1.0.0.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 http://bioconductor.org/packages/methylGSA/
Package Downloads Report Download Stats

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