Package: HiCcompare
Title: HiCcompare: Joint normalization and comparative analysis of
        multiple Hi-C datasets
Version: 1.35.0
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 = "Kellen",
           family = "Cresswell",
           role = c("aut"),
           email = "cresswellkg@vcu.edu"),
    person(given = "John",
           family = "Stansfield",
           role = c("aut"),
           email = "stansfieldjc@vcu.edu"))
Description: HiCcompare provides functions for joint normalization and
        difference detection in multiple Hi-C datasets. HiCcompare
        operates on processed Hi-C data in the form of
        chromosome-specific chromatin interaction matrices. It accepts
        three-column tab-separated text files storing chromatin
        interaction matrices in a sparse matrix format which are
        available from several sources. HiCcompare is designed to give
        the user the ability to perform a comparative analysis on the
        3-Dimensional structure of the genomes of cells in different
        biological states.`HiCcompare` differs from other packages that
        attempt to compare Hi-C data in that it works on processed data
        in chromatin interaction matrix format instead of pre-processed
        sequencing data. In addition, `HiCcompare` provides a
        non-parametric method for the joint normalization and removal
        of biases between two Hi-C datasets for the purpose of
        comparative analysis. `HiCcompare` also provides a simple yet
        robust method for detecting differences between Hi-C datasets.
Depends: R (>= 3.5.0), dplyr
Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
        GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth,
        methods, utils, graphics, pheatmap, gtools, rhdf5
Suggests: knitr, rmarkdown, testthat, multiHiCcompare
biocViews: Software, HiC, Sequencing, Normalization
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.2.3
VignetteBuilder: knitr
BugReports: https://github.com/dozmorovlab/HiCcompare/issues
URL: https://github.com/dozmorovlab/HiCcompare
Config/pak/sysreqs: libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:46:03 UTC
RemoteUrl: https://github.com/bioc/HiCcompare
RemoteRef: HEAD
RemoteSha: 52adf7edf3e32027a3b066fc46748365b48f7d86
NeedsCompilation: no
Packaged: 2026-07-04 16:06:45 UTC; root
Author: Mikhail Dozmorov [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0086-8358>),
  Kellen Cresswell [aut],
  John Stansfield [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>