Package: DMCFB
Type: Package
Title: Differentially Methylated Cytosines via a Bayesian Functional
        Approach
Version: 1.22.1
Authors@R: c(person("Farhad", "Shokoohi", role = c("aut", "cre"),
                     email = "shokoohi@icloud.com", comment = c(ORCID = "0000-0002-6224-2609"))
              )
Description: DMCFB is a pipeline for identifying differentially methylated 
    cytosines using a Bayesian functional regression model in bisulfite
    sequencing data. By using a functional regression data model, it tries to
    capture position-specific, group-specific and other covariates-specific
    methylation patterns as well as spatial correlation patterns and unknown
    underlying models of methylation data. It is robust and flexible with
    respect to the true underlying models and inclusion of any covariates, and
    the missing values are imputed using spatial correlation between positions
    and samples. A Bayesian approach is adopted for estimation and inference in
    the proposed method.
Depends: R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors,
        BiocParallel, GenomicRanges, IRanges
Imports: utils, stats, speedglm, MASS, data.table, splines, arm,
        rtracklayer, benchmarkme, tibble, matrixStats, fastDummies,
        graphics
Suggests: testthat, knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
biocViews: DifferentialMethylation, Sequencing, Coverage, Bayesian,
        Regression
License: GPL-3
Encoding: UTF-8
BugReports: https://github.com/shokoohi/DMCFB/issues
RoxygenNote: 7.3.0
git_url: https://git.bioconductor.org/packages/DMCFB
git_branch: RELEASE_3_21
git_last_commit: 6b130ee
git_last_commit_date: 2025-05-08
Repository: Bioconductor 3.21
Date/Publication: 2025-05-08
NeedsCompilation: no
Packaged: 2025-05-09 03:06:51 UTC; biocbuild
Author: Farhad Shokoohi [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6224-2609>)
Maintainer: Farhad Shokoohi <shokoohi@icloud.com>
Built: R 4.5.0; ; 2025-05-10 18:55:43 UTC; unix
