Package: HiCcompare
Title: HiCcompare: Joint normalization and comparative analysis of
        multiple Hi-C datasets
Version: 1.31.0
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
git_url: https://git.bioconductor.org/packages/HiCcompare
git_branch: devel
git_last_commit: 4f38d5c
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 23:37:58 UTC; biocbuild
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>
Built: R 4.5.0; ; 2025-06-05 13:10:17 UTC; windows
