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CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Bioconductor version: Release (3.18)

A pipeline for analysing Capture Hi-C data.

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

Maintainer: Mikhail Spivakov <mikhail.spivakov at>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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:

CHiCAGO Vignette HTML R Script
Reference Manual PDF


biocViews Epigenetics, HiC, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License Artistic-2.0
Depends R (>= 3.3.1), data.table
Imports matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils
System Requirements
See More
Suggests argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub
Linking To
Depends On Me PCHiCdata
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Chicago_1.30.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) Chicago_1.30.0.tgz
macOS Binary (arm64) Chicago_1.30.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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