Package: chicane
Title: Capture Hi-C Analysis Engine
Type: Package
Version: 0.1.8
Date: 2021-11-03
Authors@R: c(
  person("Erle", "Holgersen", role = "aut"),
  person("Olivia", "Leavy", role = "aut"),
  person("Olivia", "Fletcher", role = "aut"),
  person("Frank", "Dudbridge", role = "aut"),
  person("Syed", "Haider", role = c("aut", "cre"), email = "Syed.Haider@icr.ac.uk")
  )
Author: Erle Holgersen [aut],
  Olivia Leavy [aut],
  Olivia Fletcher [aut],
  Frank Dudbridge [aut],
  Syed Haider [aut, cre]
Maintainer: Syed Haider <Syed.Haider@icr.ac.uk>
Description: Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Depends: R (>= 3.5.0), gamlss.tr, gamlss, data.table
License: GPL-2
Encoding: UTF-8
LazyData: true
biocViews:
Imports: MASS, stats, foreach, doParallel, iterators, bedr, knitr,
        rmarkdown
SystemRequirements: bedtools
Suggests: testthat, GenomicInteractions, GenomicRanges, Gviz, countreg
Additional_repositories: http://R-Forge.R-project.org/
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-11-03 18:11:43 UTC; shaider
Repository: CRAN
Date/Publication: 2021-11-06 15:00:16 UTC
Built: R 4.6.0; ; 2026-04-28 15:38:43 UTC; unix
