dmGsea
Efficient Gene Set Enrichment Analysis for DNA Methylation Data
Bioconductor version: 3.24 · Package version: 1.3.4
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dmGsea")Details
| Maintainer | Zongli Xu <xuz@niehs.nih.gov> |
| Author | Zongli Xu [cre, aut] (ORCID: <https://orcid.org/0000-0002-9034-8902>), Alison Motsinger-Reif [aut], Liang Niu [aut] |
| License | Artistic-2.0 |
| URL | https://github.com/Bioconductor/dmGsea |
| Bug Reports | https://github.com/Bioconductor/dmGsea/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CopyNumberVariation, Coverage, DNAMethylation, GeneExpression, GeneSetEnrichment, GenomicVariation, Pathways, Proteomics, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/dmGsea/ |
Citation
From within R, enter citation("dmGsea"):
Zongli Xu, Alison Motsinger-Reif, Liang Niu. dmGsea: Efficient Gene Set Enrichment Analysis for DNA Methylation Data. doi:10.18129/B9.bioc.dmGsea, R package version 1.3.4, https://bioconductor.org/packages/dmGsea.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | dmGsea_1.3.4.tar.gz |
| Windows binary (x86_64) | dmGsea_1.3.4.zip |
| macOS binary (arm64) | dmGsea_1.3.4.tgz |
| macOS binary (x86_64) | dmGsea_1.3.4.tgz |
Dependencies
Depends: utils, stats, parallel, Matrix, SummarizedExperiment, methods, R (>= 3.5.0)
Imports: dqrng, AnnotationDbi, poolr, BiasedUrn, GenomeInfoDb
Suggests: msigdbr, org.Hs.eg.db, org.Mm.eg.db, minfi, knitr, rmarkdown, GO.db, KEGGREST, testthat, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, BiocStyle, RUnit