Package: HiCcompare
Title: HiCcompare: Joint normalization and comparative analysis of
        multiple Hi-C datasets
Version: 1.0.0
Authors@R: c(person("John", "Stansfield", email = "stansfieldjc@vcu.edu", role = c("aut", "cre")), 
    person("Mikhail", "Dozmorov", email = "mikhail.dozmorov@vcuhealth.org", role = c("aut")))
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 permutation 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, QDNAseq,
        KernSmooth, methods, utils, graphics, pheatmap, gtools
biocViews: Software, HiC, Sequencing, Normalization
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-10-31 01:28:43 UTC; biocbuild
Author: John Stansfield [aut, cre],
  Mikhail Dozmorov [aut]
Maintainer: John Stansfield <stansfieldjc@vcu.edu>
Built: R 3.4.1; ; 2018-08-17 09:09:35 UTC; unix
