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dmGsea

This is the development version of dmGsea; to use it, please install the devel version of Bioconductor.

Efficient Gene Set Enrichment Analysis for DNA Methylation Data


Bioconductor version: Development (3.22)

The R package dmGsea provides efficient gene set enrichment analysis specifically for DNA methylation data. It addresses key biases, including probe dependency and varying probe numbers per gene. The package supports Illumina 450K, EPIC, and mouse methylation arrays. Users can also apply it to other omics data by supplying custom probe-to-gene mapping annotations. dmGsea is flexible, fast, and well-suited for large-scale epigenomic studies.

Author: Zongli Xu [cre, aut] ORCID iD ORCID: 0000-0002-9034-8902 , Alison Motsinger-Reif [aut], Liang Niu [aut], Zongli Xu [fnd]

Maintainer: Zongli Xu <xuz at niehs.nih.gov>

Citation (from within R, enter citation("dmGsea")):

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("dmGsea")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews CopyNumberVariation, Coverage, DNAMethylation, GeneExpression, GeneSetEnrichment, GenomicVariation, Pathways, Proteomics, Sequencing, Software
Version 0.99.2
In Bioconductor since BioC 3.22 (R-4.5)
License Artistic-2.0
Depends utils, stats, parallel, Matrix, SummarizedExperiment, methods
Imports dqrng, AnnotationDbi, poolr, BiasedUrn
System Requirements
URL https://github.com/Bioconductor/dmGsea
Bug Reports https://github.com/Bioconductor/dmGsea/issues
See More
Suggests msigdbr, org.Hs.eg.db, org.Mm.eg.db, minfi, knitr, rmarkdown, GO.db, KEGGREST, testthat, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19
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Package Archives

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

Source Package
Windows Binary (x86_64) dmGsea_0.99.2.zip (64-bit only)
macOS Binary (x86_64) dmGsea_0.99.2.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/dmGsea
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dmGsea
Bioc Package Browser https://code.bioconductor.org/browse/dmGsea/
Package Short Url https://bioconductor.org/packages/dmGsea/
Package Downloads Report Download Stats