Package: DMRcate 3.8.0

Tim Peters

DMRcate: Methylation array and sequencing spatial analysis methods

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

Authors:Tim Peters

DMRcate_3.8.0.tar.gz
DMRcate_3.8.0.zip(r-4.7-any)DMRcate_3.8.0.zip(r-4.6-any)DMRcate_3.8.0.zip(r-4.5-any)
DMRcate_3.8.0.tgz(r-4.6-any)DMRcate_3.8.0.tgz(r-4.5-any)
DMRcate_3.8.0.tar.gz(r-4.7-any)DMRcate_3.8.0.tar.gz(r-4.6-any)
DMRcate_3.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DMRcate/json (API)

# Install 'DMRcate' in R:
install.packages('DMRcate', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:DMRcate-3.9.0(bioc 3.24)DMRcate-3.8.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

differentialmethylationgeneexpressionmicroarraymethylationarraygeneticsdifferentialexpressiongenomeannotationdnamethylationonechanneltwochannelmultiplecomparisonqualitycontroltimecoursesequencingwholegenomeepigeneticscoveragepreprocessingdataimport

6.13 score 2 packages 533 scripts 2.1k downloads 132 mentions 14 exports 214 dependencies

Last updated from:14f31424e6 (on RELEASE_3_23). Checks:9 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR1335
linux-develERROR1784
source / vignettesERROR1912
linux-releaseERROR1769
macos-releaseERROR1522
macos-oldrelERROR1325
windows-develERROR1231
windows-releaseERROR1373
windows-oldrelERROR1504
wasm-releaseOK1106

Exports:changeFDRcpg.annotateDMR.plotdmrcateextractCoordsextractRangesfitParallelgetCollapsedBetasKernelSumsKernelTestrmSNPandCHSegmentsequencing.annotateSparseDeltas

Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassassortheadbackportsbase64base64encbeachmatbeanplotBHBiasedUrnBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibbsseqbumphuntercachemcheckmatecigarilloclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdichromatdigestdir.expirydoRNGdplyredgeRensembldbevaluateExperimentHubfarverfastmapFDb.InfiniumMethylation.hg19filelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2glueGO.dbgridExtragtablegtoolsGvizh5mreadHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaiointerpIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimimeminfimissMethylmulttestnlmennetnor1mixopensslorg.Hs.eg.dbpermutepillarpkgconfigplyrpngpreprocessCoreprettyunitsprogressProtGenericspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerruvrvestS4ArraysS4VectorsS7sassscalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryaml