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>
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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, GeneRegulation, GeneSetEnrichment, Pathways, Regression, Software |
| Version | 1.2.3 |
| 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, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.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_1.2.3.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 |
| 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 3.9 | Source Archive |