Package: DMCFB Type: Package Title: Differentially Methylated Cytosines via a Bayesian Functional Approach Version: 1.26.0 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: Bioconductor 3.23 Date/Publication: 2026-04-28 12:51:04 UTC RemoteUrl: https://github.com/bioc/DMCFB RemoteRef: RELEASE_3_23 RemoteSha: b584dc0700c30521e3931ad3c94effe0dc65919f NeedsCompilation: no Packaged: 2026-10-11 08:08:30 UTC; root Author: Farhad Shokoohi [aut, cre] (ORCID: ) Maintainer: Farhad Shokoohi