Package: segmentSeq
Type: Package
Title: Methods for identifying small RNA loci from high-throughput
        sequencing data
Version: 2.45.0
Date: 2025-07-23
Authors@R: c(person("Thomas J.", "Hardcastle", role = "aut"),
  person("Samuel", "Granjeaud", role = "cre", email = "samuel.granjeaud@inserm.fr", comment=c(ORCID="0000-0001-9245-1535")))
Description: High-throughput sequencing technologies allow the
        production of large volumes of short sequences, which can be
        aligned to the genome to create a set of matches to the genome.
        By looking for regions of the genome which to which there are
        high densities of matches, we can infer a segmentation of the
        genome into regions of biological significance. The methods in
        this package allow the simultaneous segmentation of data from
        multiple samples, taking into account replicate data, in order
        to create a consensus segmentation. This has obvious
        applications in a number of classes of sequencing experiments,
        particularly in the discovery of small RNA loci and novel mRNA
        transcriptome discovery.
License: GPL-3
LazyLoad: yes
Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
        GenomicRanges, ShortRead, stats
Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown
Imports: Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind
biocViews: MultipleComparison, Sequencing, Alignment,
        DifferentialExpression, QualityControl, DataImport
URL: https://github.com/samgg/segmentSeq
BugReports: https://github.com/samgg/segmentSeq/issues
VignetteBuilder: knitr
Config/pak/sysreqs: libbz2-dev libjpeg-dev liblzma-dev libpng-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:04:32 UTC
RemoteUrl: https://github.com/bioc/segmentSeq
RemoteRef: HEAD
RemoteSha: a33a34ab5e73dccb3a41ccf71d75a91f113f028a
NeedsCompilation: no
Packaged: 2026-02-22 08:11:01 UTC; root
Author: Thomas J. Hardcastle [aut],
  Samuel Granjeaud [cre] (ORCID: <https://orcid.org/0000-0001-9245-1535>)
Maintainer: Samuel Granjeaud <samuel.granjeaud@inserm.fr>
Built: R 4.6.0; ; 2026-02-22 08:13:09 UTC; windows
