DESCRIPTION

Package: hicrep
Title: Measuring the reproducibility of Hi-C data
Version: 1.12.0
Authors@R: c(person("Tao", "Yang", email = "xadmyangt@gmail.com", role =
        c("aut", "cre")), person("Fan", "Song", email = "songfudan@gmail.com"
        , role = c("ctb")))
Description: Hi-C is a powerful technology for studying genome-wide
        chromatin interactions. However, current methods for assessing
        Hi-C data reproducibility can produce misleading results
        because they ignore spatial features in Hi-C data, such as
        domain structure and distance-dependence. We present a novel
        reproducibility measure that systematically takes these
        features into consideration. This measure can assess pairwiseß
        differences between Hi-C matrices under a wide range of
        settings, and can be used to determine optimal sequencing
        depth. Compared to existing approaches, it consistently shows
        higher accuracy in distinguishing subtle differences in
        reproducibility and depicting interrelationships of cell
        lineages than existing approaches. This R package `hicrep`
        implements our approach.
biocViews: Sequencing, HiC, QualityControl
Depends: R (>= 3.3)
Imports: stats, rhdf5, Rcpp, rmarkdown, testthat
License: GPL (>= 2.0)
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-02-24 13:04:30 UTC
Author: Tao Yang [aut, cre], Fan Song [ctb]
Maintainer: Tao Yang <xadmyangt@gmail.com>
RoxygenNote: 6.1.1