Package: segmenter
Type: Package
Title: Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
Version: 1.19.0
Description: Chromatin segmentation analysis transforms ChIP-seq data
        into signals over the genome. The latter represents the
        observed states in a multivariate Markov model to predict the
        chromatin's underlying states. ChromHMM, written in Java,
        integrates histone modification datasets to learn the chromatin
        states de-novo. The goal of this package is to call chromHMM
        from within R, capture the output files in an S4 object and
        interface to other relevant Bioconductor analysis tools. In
        addition, segmenter provides functions to test, select and
        visualize the output of the segmentation.
Authors@R: person("Mahmoud", "Ahmed",
                  email = "mahmoud.s.fahmy@students.kasralainy.edu.eg",
                  role = c("aut", "cre"),
                  comment = c(ORCID = "0000-0002-4377-6541"))
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
Depends: R (>= 4.1)
BugReports: https://github.com/MahShaaban/segmenter/issues
Suggests: testthat, knitr, rmarkdown,
        TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges,
        S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils,
        methods, chromhmmData
VignetteBuilder: knitr
biocViews: Software, HistoneModification
LazyData: True
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:56:25 UTC
RemoteUrl: https://github.com/bioc/segmenter
RemoteRef: HEAD
RemoteSha: da0c05d2e3fffd5eeb137650d84f372371354f34
NeedsCompilation: no
Packaged: 2026-07-10 10:21:08 UTC; root
Author: Mahmoud Ahmed [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>