Package: dmrseq 1.32.0

Keegan Korthauer

dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.

Authors:Keegan Korthauer [cre, aut], Rafael Irizarry [aut], Yuval Benjamini [aut], Sutirtha Chakraborty [aut]

dmrseq_1.32.0.tar.gz
dmrseq_1.32.0.zip(r-4.7)dmrseq_1.32.0.zip(r-4.6)dmrseq_1.32.0.zip(r-4.5)
dmrseq_1.32.0.tgz(r-4.6-any)dmrseq_1.32.0.tgz(r-4.5-any)
dmrseq_1.32.0.tar.gz(r-4.7-any)dmrseq_1.32.0.tar.gz(r-4.6-any)
dmrseq_1.32.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dmrseq/json (API)
NEWS

# Install 'dmrseq' in R:
install.packages('dmrseq', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • annot.chr21 - Annot.chr21: Annotation information for chromosome 21, hg38 genome
  • BS.chr21 - BS.chr21: Whole-genome bisulfite sequencing for chromosome 21 from Lister et al.
  • dmrs.ex - Dmrs.ex: Example results of DMRs

On BioConductor:dmrseq-1.33.0(bioc 3.24)dmrseq-1.32.0(bioc 3.23)

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

immunooncologydnamethylationepigeneticsmultiplecomparisonsoftwaresequencingdifferentialmethylationwholegenomeregressionfunctionalgenomics

6.51 score 1 packages 102 scripts 728 downloads 7 mentions 6 exports 139 dependencies

Last updated from:c4da253810 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING289
linux-devel-x86_64NOTE614
source / vignettesOK458
linux-release-x86_64NOTE499
macos-release-arm64NOTE306
macos-oldrel-arm64NOTE307
windows-develNOTE616
windows-releaseNOTE563
windows-oldrelNOTE655
wasm-releaseOK208

Exports:dmrseqgetAnnotmeanDiffplotDMRsplotEmpiricalDistributionsimDMRs

Dependencies:abindAnnotationDbiAnnotationHubannotatraskpassassortheadbeachmatBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebsseqbumphuntercachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablegtoolsh5mreadHDF5Arrayhmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopenssloutlierspermutepillarpkgconfigplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryaml

Analyzing Bisulfite-seq data with dmrseq

Keegan Korthauer

Rendered fromdmrseq.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2024-09-24
Started: 2017-07-21