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: 0.1.1
Depends: R (≥ 3.5.0), gamlss.tr, gamlss
Imports: data.table, MASS, stats, foreach, doParallel, iterators
Suggests: knitr, rmarkdown, testthat, GenomicInteractions, Gviz, countreg
Published: 2019-10-01
Author: Erle Holgersen [aut, cre], Olivia Leavy [aut], Olivia Fletcher [aut], Frank Dudbridge [aut], Syed Haider [aut]
Maintainer: Erle Holgersen <erle.holgersen at gmail.com>
License: GPL-2
NeedsCompilation: no
SystemRequirements: bedtools
Materials: NEWS
CRAN checks: chicane results

Downloads:

Reference manual: chicane.pdf
Vignettes: Introduction
Visualising Interactions
Package source: chicane_0.1.1.tar.gz
Windows binaries: r-devel: chicane_0.1.1.zip, r-release: chicane_0.1.1.zip, r-oldrel: chicane_0.1.1.zip
OS X binaries: r-release: chicane_0.1.1.tgz, r-oldrel: chicane_0.1.1.tgz
Old sources: chicane archive

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