methylGSA
Gene Set Analysis Using the Outcome of Differential Methylation
Bioconductor version: Release (3.19)
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("methylGSA")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software |
Version | 1.22.0 |
In Bioconductor since | BioC 3.8 (R-3.5) (6 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_1.22.0.tar.gz |
Windows Binary | methylGSA_1.22.0.zip |
macOS Binary (x86_64) | methylGSA_1.22.0.tgz |
macOS Binary (arm64) | methylGSA_1.22.0.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 |