DESCRIPTION

Package: HiCcompare
Title: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
Version: 1.23.1
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 (>= 3.4.0),
    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