Package: dmrseq 1.25.0
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:
dmrseq_1.25.0.tar.gz
dmrseq_1.25.0.zip(r-4.5)dmrseq_1.25.0.zip(r-4.4)dmrseq_1.25.0.zip(r-4.3)
dmrseq_1.25.0.tgz(r-4.4-any)dmrseq_1.25.0.tgz(r-4.3-any)
dmrseq_1.25.0.tar.gz(r-4.5-noble)dmrseq_1.25.0.tar.gz(r-4.4-noble)
dmrseq_1.25.0.tgz(r-4.4-emscripten)dmrseq_1.25.0.tgz(r-4.3-emscripten)
dmrseq.pdf |dmrseq.html✨
dmrseq/json (API)
NEWS
| # Install 'dmrseq' in R: |
| install.packages('dmrseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- BS.chr21 - BS.chr21: Whole-genome bisulfite sequencing for chromosome 21 from Lister et al.
- annot.chr21 - Annot.chr21: Annotation information for chromosome 21, hg38 genome
- dmrs.ex - Dmrs.ex: Example results of DMRs
On BioConductor:dmrseq-1.25.0(bioc 3.20)dmrseq-1.24.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:0ee8f6692e
Exports:dmrseqgetAnnotmeanDiffplotDMRsplotEmpiricalDistributionsimDMRs
Dependencies:abindAnnotationDbiAnnotationHubannotatraskpassbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebsseqbumphuntercachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablegtoolsHDF5ArrayhmshttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopenssloutlierspermutepillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryamlzlibbioc
