Package: mCSEA 1.27.2
Jordi Martorell-Marugán
mCSEA: Methylated CpGs Set Enrichment Analysis
Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.
Authors:
mCSEA_1.27.2.tar.gz
mCSEA_1.27.2.zip(r-4.5)mCSEA_1.27.2.zip(r-4.4)mCSEA_1.27.2.zip(r-4.3)
mCSEA_1.27.2.tgz(r-4.4-any)mCSEA_1.27.2.tgz(r-4.3-any)
mCSEA_1.27.2.tar.gz(r-4.5-noble)mCSEA_1.27.2.tar.gz(r-4.4-noble)
mCSEA_1.27.2.tgz(r-4.4-emscripten)mCSEA_1.27.2.tgz(r-4.3-emscripten)
mCSEA.pdf |mCSEA.html✨
mCSEA/json (API)
NEWS
| # Install 'mCSEA' in R: |
| install.packages('mCSEA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:mCSEA-1.27.1(bioc 3.21)mCSEA-1.25.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologydifferentialmethylationdnamethylationepigeneticsgeneticsgenomeannotationmethylationarraymicroarraymultiplecomparisontwochannel
Last updated 19 days agofrom:641202dafb. Checks:ERROR: 3 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Dec 04 2024 |
| R-4.5-win | WARNING | Dec 04 2024 |
| R-4.5-linux | WARNING | Dec 04 2024 |
| R-4.4-win | WARNING | Dec 04 2024 |
| R-4.4-mac | WARNING | Dec 04 2024 |
| R-4.3-win | ERROR | Dec 04 2024 |
| R-4.3-mac | ERROR | Dec 04 2024 |
Exports:mCSEAIntegratemCSEAPlotmCSEAPlotGSEAmCSEATestrankProbes
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGO.dbgraphgridExtragtableGvizhighrHmischmsHomo.sapienshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmCSEAdatamemoisemgcvmimemunsellnlmennetopensslorg.Hs.eg.dbOrganismDbipillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Methylated CpGs Set Enrichment Analysis | mCSEA-package mCSEA |
| Expression data example | exprTest |
| Integrate methylation and expression | mCSEAIntegrate |
| Plot mCSEA results | mCSEAPlot |
| Plot mCSEA results | mCSEAPlotGSEA |
| mCSEA core analysis | mCSEATest |
| Precomputed mCSEA results | myRank myResults precomputedmCSEA |
| Rank CpG probes | rankProbes |
