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]
, Alison Motsinger-Reif [aut], Liang Niu [aut], Zongli Xu [fnd]
Maintainer: Zongli Xu <xuz at niehs.nih.gov>
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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dmGsea")| dmGsea User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, DNAMethylation, GeneExpression, GeneSetEnrichment, GenomicVariation, Pathways, Proteomics, Sequencing, Software |
| Version | 0.99.3 |
| 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, BiocStyle, RUnit |
| 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 | dmGsea_0.99.3.tar.gz |
| Windows Binary (x86_64) | dmGsea_0.99.3.zip |
| macOS Binary (x86_64) | dmGsea_0.99.3.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 |