DOI: 10.18129/B9.bioc.Chicago    

This is the development version of Chicago; for the stable release version, see Chicago.

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Bioconductor version: Development (3.9)

A pipeline for analysing Capture Hi-C data.

Author: Jonathan Cairns, Paula Freire Pritchett, Steven Wingett, Mikhail Spivakov

Maintainer: Mikhail Spivakov <spivakov at>

Citation (from within R, enter citation("Chicago")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("Chicago", version = "3.9")

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script CHiCAGO Vignette
PDF   Reference Manual
Text   NEWS


biocViews Epigenetics, HiC, ImmunoOncology, Sequencing, Software
Version 1.11.1
In Bioconductor since BioC 3.3 (R-3.3) (3 years)
License Artistic-2.0
Depends R (>= 3.2), data.table
Imports matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils
Suggests argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub
Depends On Me PCHiCdata
Imports Me
Suggests Me
Links To Me
Build Report  

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Follow Installation instructions to use this package in your R session.

Source Package Chicago_1.11.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) Chicago_1.11.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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