Package: DMCFB
Type: Package
Title: Differentially Methylated Cytosines via a Bayesian Functional
        Approach
Version: 1.24.0
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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:54:42 UTC
RemoteUrl: https://github.com/bioc/DMCFB
RemoteRef: RELEASE_3_22
RemoteSha: 0f829bfbf3ef03e02aa7b046e13be80f417b9a4b
NeedsCompilation: no
Packaged: 2025-11-11 14:04:05 UTC; root
Author: Farhad Shokoohi [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6224-2609>)
Maintainer: Farhad Shokoohi <shokoohi@icloud.com>
Built: R 4.5.2; ; 2025-11-11 14:13:50 UTC; windows
