Introduction | List of functions | Example Analysis | Example 1: Differentially methylated probes from EWAS | Example 2: Enrichment analysis for arrays other than 450K and EPIC | Example 3: Enrichment analysis with user provided geneset | Example 4: Enrichment analysis for gene expression type of data that do not | need to combine test statistics | Gene set and pathway databases | Kyoto Encyclopedia of Genes and Genomes (KEGG) | Gene Ontology (GO) | The Molecular Signatures Database (MSigDB) | Reactome | Types of gene set enrichment analyses | Method options to combine p-value: | References
Package: dmGsea 1.3.1
Zongli Xu
dmGsea: Efficient Gene Set Enrichment Analysis for DNA Methylation Data
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.
Authors:
dmGsea_1.3.1.tar.gz
dmGsea_1.3.1.zip(r-4.7)dmGsea_1.3.1.zip(r-4.6)dmGsea_1.3.1.zip(r-4.5)
dmGsea_1.3.1.tgz(r-4.6-any)dmGsea_1.3.1.tgz(r-4.5-any)
dmGsea_1.3.1.tar.gz(r-4.7-any)dmGsea_1.3.1.tar.gz(r-4.6-any)
dmGsea_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dmGsea/json (API)
| # Install 'dmGsea' in R: |
| install.packages('dmGsea', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:dmGsea-1.3.1(bioc 3.24)dmGsea-1.2.1(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
genesetenrichmentpathwaysdnamethylationproteomicssequencingcopynumbervariationgeneexpressiongenomicvariationcoverage
Last updated from:67d9347086. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 433 | ||
| linux-devel-x86_64 | OK | 698 | ||
| source / vignettes | OK | 584 | ||
| linux-release-x86_64 | OK | 766 | ||
| macos-release-arm64 | OK | 415 | ||
| macos-oldrel-arm64 | OK | 448 | ||
| windows-devel | OK | 575 | ||
| windows-release | OK | 572 | ||
| windows-oldrel | OK | 434 | ||
| wasm-release | OK | 427 |
Exports:geneID2geneNamegetGOgetIlluminaAnnotationgetKEGGgetMSigDBgetReactomegsGenegsPGgsProbegsRank
Dependencies:abindAnnotationDbiaskpassBHBiasedUrnBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIDelayedArraydqrngfastmapgenericsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlatticelifecyclemathjaxrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngpoolrR6RcpprlangRSQLiteS4ArraysS4VectorsSeqinfositmoSparseArraySummarizedExperimentsysvctrsXVector
