Package: HiCcompare
Title: HiCcompare: Joint normalization and comparative analysis of
        multiple Hi-C datasets
Version: 1.18.0
Author: John Stansfield <stansfieldjc@vcu.edu>,
    Kellen Cresswell <cresswellkg@vcu.edu>,
    Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>
Maintainer: John Stansfield <stansfieldjc@vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>
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, QDNAseq,
        KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
biocViews: Software, HiC, Sequencing, Normalization
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, testthat, multiHiCcompare
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: RELEASE_3_15
git_last_commit: 27235fc
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
NeedsCompilation: no
Packaged: 2022-04-26 23:14:54 UTC; biocbuild
Built: R 4.2.0; ; 2022-04-27 09:36:12 UTC; windows
