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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 (3.18)

A pipeline for analysing Capture Hi-C data.

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

Maintainer: Mikhail Spivakov <mikhail.spivakov at lms.mrc.ac.uk>

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

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Chicago")

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

Documentation

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

browseVignettes("Chicago")
CHiCAGO Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Epigenetics, HiC, Sequencing, Software
Version 1.29.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License Artistic-2.0
Depends R (>= 3.3.1), data.table
Imports matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils
Linking To
Suggests argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub
System Requirements
Enhances
URL
See More
Depends On Me PCHiCdata
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package Chicago_1.29.0.tar.gz
Windows Binary Chicago_1.29.0.zip
macOS Binary (x86_64) Chicago_1.29.0.tgz
macOS Binary (arm64) Chicago_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Chicago
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Chicago
Bioc Package Browser https://code.bioconductor.org/browse/Chicago/
Package Short Url https://bioconductor.org/packages/Chicago/
Package Downloads Report Download Stats