Package: HiCExperiment
Title: Bioconductor class for interacting with Hi-C files in R
Version: 1.12.0
Date: 2025-07-22
Authors@R: 
    c(person(given = "Jacques",
           family = "Serizay",
           role = c("aut", "cre"),
           email = "jacquesserizay@gmail.com",
           comment = c(ORCID = "0000-0002-4295-0624")))
Description: R generic interface to Hi-C contact matrices in
        `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other
        Hi-C processed file formats. Contact matrices can be partially
        parsed using a random access method, allowing a
        memory-efficient representation of Hi-C data in R. The
        `HiCExperiment` class stores the Hi-C contacts parsed from
        local contact matrix files. `HiCExperiment` instances can be
        further investigated in R using the `HiContacts` analysis
        package.
License: MIT + file LICENSE
URL: https://github.com/js2264/HiCExperiment
BugReports: https://github.com/js2264/HiCExperiment/issues
Depends: R (>= 4.2)
Imports: InteractionSet, strawr, Seqinfo, GenomicRanges, IRanges,
        S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5,
        Matrix, vroom, dplyr, stats
Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer,
        testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
biocViews: HiC, DNA3DStructure, DataImport
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Collate: 'HiCExperiment-class.R' 'AggrHiCExperiment-class.R'
        'AllGenerics.R' 'HiCExperiment-methods.R'
        'AggrHiCExperiment-methods.R' 'PairsFile-class.R'
        'ContactsFile-class.R' 'ContactsFile-methods.R'
        'CoolFile-class.R' 'CoolFile-methods.R' 'HicFile-class.R'
        'HicFile-methods.R' 'HicproFile-class.R' 'HicproFile-methods.R'
        'PairsFile-methods.R' 'import-methods.R' 'available.R' 'bin.R'
        'checks.R' 'coerce.R' 'data.R' 'export-methods.R' 'globals.R'
        'parse-cool.R' 'parse-hic.R' 'parse-hicpro.R' 'parse-pairs.R'
        'parse-slices.R' 'reexports.R' 'utils.R' 'zzz.R'
Config/pak/sysreqs: libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:00:01 UTC
RemoteUrl: https://github.com/bioc/HiCExperiment
RemoteRef: RELEASE_3_23
RemoteSha: f4d282bae2901f9fd1f786ca61afd1ea04145e29
NeedsCompilation: no
Packaged: 2026-04-29 15:04:59 UTC; root
Author: Jacques Serizay [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4295-0624>)
Maintainer: Jacques Serizay <jacquesserizay@gmail.com>
Built: R 4.6.0; ; 2026-04-29 15:09:40 UTC; windows
