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, 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>
License: GPL-2
NeedsCompilation: no
SystemRequirements: bedtools
Materials: NEWS
CRAN checks: chicane results


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


Package source: chicane_0.1.8.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
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


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