Package: dmrseq
Type: Package
Title: Detection and inference of differentially methylated regions
        from Whole Genome Bisulfite Sequencing
Version: 1.31.0
Authors@R: c(person("Keegan", "Korthauer", role = c("cre", "aut"), 
                    email = "keegan@stat.ubc.ca", 
                    comment = c(ORCID = "0000-0002-4565-1654")),
             person("Rafael", "Irizarry", role = "aut",
                    email = "rafa@jimmy.harvard.edu",
                    comment = c(ORCID = "0000-0002-3944-4309")),
             person("Yuval", "Benjamini", role = "aut"),
             person("Sutirtha", "Chakraborty", role = "aut"))
Description: 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.
License: MIT + file LICENSE
Depends: R (>= 3.5), bsseq
Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer,
        bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats,
        BiocParallel, outliers, methods, locfit, IRanges, grDevices,
        graphics, stats, utils, annotatr, AnnotationHub, rtracklayer,
        Seqinfo, splines
Suggests: knitr, rmarkdown, BiocStyle,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
biocViews: ImmunoOncology, DNAMethylation, Epigenetics,
        MultipleComparison, Software, Sequencing,
        DifferentialMethylation, WholeGenome, Regression,
        FunctionalGenomics
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:43:32 UTC
RemoteUrl: https://github.com/bioc/dmrseq
RemoteRef: HEAD
RemoteSha: 4df1200aaf61a0cc13a01922ad4e34b80e52f830
NeedsCompilation: no
Packaged: 2026-03-10 08:35:39 UTC; root
Author: Keegan Korthauer [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-4565-1654>),
  Rafael Irizarry [aut] (ORCID: <https://orcid.org/0000-0002-3944-4309>),
  Yuval Benjamini [aut],
  Sutirtha Chakraborty [aut]
Maintainer: Keegan Korthauer <keegan@stat.ubc.ca>
Built: R 4.6.0; ; 2026-03-10 08:39:03 UTC; windows
