Package: DMRScan
Title: Detection of Differentially Methylated Regions
Version: 1.30.0
Authors@R: c( person("CM", "Page", email = "page.ntnu@gmail.com", role =
    c("aut","cre")), person("L", "Vos", email = "Linda.Vos@Kreftregisteret.no",
    role = "aut"), person("TB", "Rounge", email = "", role = "ctb"), person("HF", "Harbo", email = "", role = "ths"), 
	person("BK", "Andreassen", email = "Bettina.Kulle.Andreassen@Kreftregisteret.no", role = "aut"))
Description: This package detects significant differentially methylated regions
    (for both qualitative and quantitative traits), using a scan statistic with
    underlying Poisson heuristics. The scan statistic will depend on a sequence of
    window sizes (# of CpGs within each window) and on a threshold for each window
    size. This threshold can be calculated by three different means: i) analytically
    using Siegmund et.al (2012) solution (preferred), ii) an important sampling as
    suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing
    between a number of different options for modeling the dependency between each
    CpG.
biocViews: Software, Technology, Sequencing, WholeGenome
Depends: R (>= 3.6.0)
Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb,
        methods, mvtnorm, stats, parallel
License: GPL-3
LazyData: true
Author: Christian M Page [aut, cre],
    Linda Vos [aut],
    Trine B Rounge [ctb, dtc],
    Hanne F Harbo [ths],
    Bettina K Andreassen [aut]
Maintainer: Christian M Page <page.ntnu@gmail.com>
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, BiocStyle, BiocManager
VignetteBuilder: knitr
URL: https://github.com/christpa/DMRScan
BugReports: https://github.com/christpa/DMRScan/issues
PackageStatus: Active
git_url: https://git.bioconductor.org/packages/DMRScan
git_branch: RELEASE_3_21
git_last_commit: b3a7b14
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 00:18:22 UTC; biocbuild
Built: R 4.5.0; ; 2025-04-16 14:20:48 UTC; windows
