Package: multiHiCcompare
Title: Normalize and detect differences between Hi-C datasets when replicates 
  of each experimental condition are available
Version: 1.29.0
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
git_url: https://git.bioconductor.org/packages/multiHiCcompare
git_branch: devel
git_last_commit: 31f6781
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
