Package: DMRcate 3.3.0
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:
DMRcate_3.3.0.tar.gz
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DMRcate_3.3.0.tgz(r-4.4-any)
DMRcate_3.3.0.tar.gz(r-4.5-noble)DMRcate_3.3.0.tar.gz(r-4.4-noble)
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DMRcate.pdf |DMRcate.html✨
DMRcate/json (API)
NEWS
| # Install 'DMRcate' in R: |
| install.packages('DMRcate', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:DMRcate-3.3.0(bioc 3.21)DMRcate-3.2.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
differentialmethylationgeneexpressionmicroarraymethylationarraygeneticsdifferentialexpressiongenomeannotationdnamethylationonechanneltwochannelmultiplecomparisonqualitycontroltimecoursesequencingwholegenomeepigeneticscoveragepreprocessingdataimport
Last updated 2 months agofrom:665b0ce7b6. Checks:ERROR: 2 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | ERROR | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
Exports:changeFDRcpg.annotateDMR.plotdmrcateextractCoordsextractRangesfitParallelgetCollapsedBetasKernelSumsKernelTestrmSNPandCHSegmentsequencing.annotateSparseDeltas
Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassassortheadbackportsbase64base64encbeachmatbeanplotBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibbsseqbumphuntercachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdichromatdigestdoRNGdplyredgeRensembldbevaluateExperimentHubfansifarverfastmapFDb.InfiniumMethylation.hg19filelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2glueGO.dbgridExtragtablegtoolsGvizHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaiointerpIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimissMethylmulttestmunsellnlmennetnor1mixopensslorg.Hs.eg.dbpermutepillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogressProtGenericspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerruvrvestS4ArraysS4VectorssassscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DMR calling from bisulfite sequencing and Illumina array data | DMRcate-package DMRcate |
| Change the individual CpG FDR thresholding for a CpGannotated object. | changeFDR |
| Annotate Illumina CpGs with their chromosome position and test statistic | cpg.annotate |
| An object summarising individual CpG sites fitted to a given model | CpGannotated-class |
| Plotting DMRs | DMR.plot plot |
| DMR identification | dmrcate |
| Initial storage object for called DMRs - class | DMResults-class |
| Create a GRanges object from 'dmrcate' output. | extractRanges |
| Extract a beta matrix from a CpGannotated object. | getCollapsedBetas |
| Filter probes | rmSNPandCH |
| Annotate a bisulfite sequencing experiment (WGBS or RRBS) with probe weights and chromosomal position. | sequencing.annotate |
