Package: multiHiCcompare
Title: Normalize and detect differences between Hi-C datasets when
        replicates of each experimental condition are available
Version: 1.28.0
Authors@R: c(
    person(given = "Mikhail",
           family = "Dozmorov",
           role = c("aut", "cre"),
           email = "mikhail.dozmorov@gmail.com",
           comment = c(ORCID = "0000-0002-0086-8358")),
    person(given = "John",
           family = "Stansfield",
           role = c("aut"),
           email = "stansfieldjc@vcu.edu"))
Description: multiHiCcompare provides functions for joint normalization
        and difference detection in multiple Hi-C datasets. This
        extension of the original HiCcompare package now allows for
        Hi-C experiments with more than 2 groups and multiple samples
        per group. multiHiCcompare operates on processed Hi-C data in
        the form of sparse upper triangular matrices. It accepts four
        column (chromosome, region1, region2, IF) tab-separated text
        files storing chromatin interaction matrices. multiHiCcompare
        provides cyclic loess and fast loess (fastlo) methods adapted
        to jointly normalizing Hi-C data. Additionally, it provides a
        general linear model (GLM) framework adapting the edgeR package
        to detect differences in Hi-C data in a distance dependent
        manner.
Depends: R (>= 4.0.0)
Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman,
        pheatmap, methods, GenomicRanges, graphics, stats, utils,
        pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation
biocViews: Software, HiC, Sequencing, Normalization
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat, BiocStyle
RoxygenNote: 7.1.1
VignetteBuilder: knitr
BugReports: https://github.com/dozmorovlab/multiHiCcompare/issues
URL: https://github.com/dozmorovlab/multiHiCcompare
Config/pak/sysreqs: libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:46:53 UTC
RemoteUrl: https://github.com/bioc/multiHiCcompare
RemoteRef: RELEASE_3_22
RemoteSha: 5d0766c2438a6d9d30d2b5392833d9ac2a1eb00e
NeedsCompilation: no
Packaged: 2026-02-03 08:58:10 UTC; root
Author: Mikhail Dozmorov [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0086-8358>),
  John Stansfield [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Built: R 4.5.2; ; 2026-02-03 09:00:12 UTC; windows
