Package: SOMNiBUS
Title: Smooth modeling of bisulfite sequencing
Version: 1.21.0
Authors@R: c(person("Kaiqiong", "Zhao", role = "aut", 
                    email = "kaiqiong.zhao@mail.mcgill.ca"),
             person("Kathleen", "Klein", role = "cre",
                    email = "kathleen.klein@mail.mcgill.ca"),
             person("Audrey", "Lemaçon", role = c("ctb","ctr"), 
                    email = "audrey@mims.ai"),
             person("Simon", "Laurin-Lemay", role = c("ctb","ctr"),
                    email = "simon@mims.ai"),
             person("My Intelligent Machines Inc.", role = "ctr"),
             person("Celia", "Greenwood" , role = c("ths", "aut"), 
                    email = "celia.greenwood@mcgill.ca")
                    )
Description: This package aims to analyse count-based methylation data
        on predefined genomic regions, such as those obtained by
        targeted sequencing, and thus to identify differentially
        methylated regions (DMRs) that are associated with phenotypes
        or traits. The method is built a rich flexible model that
        allows for the effects, on the methylation levels, of multiple
        covariates to vary smoothly along genomic regions. At the same
        time, this method also allows for sequencing errors and can
        adjust for variability in cell type mixture.
License: MIT + file LICENSE
URL: https://github.com/kaiqiong/SOMNiBUS
BugReports: https://github.com/kaiqiong/SOMNiBUS/issues
Depends: R (>= 4.1.0)
Imports: Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb,
        GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr,
        yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr,
Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown,
        testthat, TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
VignetteBuilder: knitr
biocViews: DNAMethylation, Regression, Epigenetics,
        DifferentialMethylation, Sequencing, FunctionalPrediction
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
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: 2026-04-28 12:54:52 UTC
RemoteUrl: https://github.com/bioc/SOMNiBUS
RemoteRef: HEAD
RemoteSha: 8ae13398aefe404f3015729a8c235a6dbb9c6c98
NeedsCompilation: no
Packaged: 2026-07-03 23:50:39 UTC; root
Author: Kaiqiong Zhao [aut],
  Kathleen Klein [cre],
  Audrey Lemaçon [ctb, ctr],
  Simon Laurin-Lemay [ctb, ctr],
  My Intelligent Machines Inc. [ctr],
  Celia Greenwood [ths, aut]
Maintainer: Kathleen Klein <kathleen.klein@mail.mcgill.ca>