Package: segmenter
Type: Package
Title: Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
Version: 1.12.0
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
git_url: https://git.bioconductor.org/packages/segmenter
git_branch: RELEASE_3_20
git_last_commit: c64c4ca
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 02:54:22 UTC; biocbuild
Author: Mahmoud Ahmed [aut, cre] (<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
Built: R 4.4.2; ; 2025-01-04 01:25:11 UTC; unix
