chicane: Capture Hi-C Analysis Engine

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.

Version:	0.1.8
Depends:	R (≥ 3.5.0), gamlss.tr, gamlss, data.table
Imports:	MASS, stats, foreach, doParallel, iterators, bedr, knitr, rmarkdown
Suggests:	testthat, GenomicInteractions, GenomicRanges, Gviz, countreg
Published:	2021-11-06
DOI:	10.32614/CRAN.package.chicane
Author:	Erle Holgersen [aut], Olivia Leavy [aut], Olivia Fletcher [aut], Frank Dudbridge [aut], Syed Haider [aut, cre]
Maintainer:	Syed Haider <Syed.Haider at icr.ac.uk>
License:	GPL-2
NeedsCompilation:	no
SystemRequirements:	bedtools
Additional_repositories:	http://R-Forge.R-project.org/
Materials:	NEWS
CRAN checks:	chicane results

Documentation:

Reference manual:	chicane.pdf
Vignettes:	Getting Started Visualising Interactions

Downloads:

Package source:	chicane_0.1.8.tar.gz
Windows binaries:	r-devel: chicane_0.1.8.zip, r-release: chicane_0.1.8.zip, r-oldrel: chicane_0.1.8.zip
macOS binaries:	r-release (arm64): chicane_0.1.8.tgz, r-oldrel (arm64): chicane_0.1.8.tgz, r-release (x86_64): chicane_0.1.8.tgz, r-oldrel (x86_64): chicane_0.1.8.tgz
Old sources:	chicane archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=chicane to link to this page.