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Showing content from https://www.bioconductor.org/packages/devel/data/annotation/html/../../../bioc/html/methylGSA.html below:

Bioconductor - methylGSA (development version)

methylGSA

This is the development version of methylGSA; for the stable release version, see methylGSA.

Gene Set Analysis Using the Outcome of Differential Methylation

Bioconductor version: Development (3.22)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.27.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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 Package Archives

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

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