Chicago

DOI: 10.18129/B9.bioc.Chicago    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Chicago.

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Bioconductor version: 3.8

A pipeline for analysing Capture Hi-C data.

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

Maintainer: Mikhail Spivakov <spivakov at babraham.ac.uk>

Installation

To install this package, start R (version "3.5") and enter:

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

 

HTML	R Script	CHiCAGO Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Epigenetics, HiC, ImmunoOncology, Sequencing, Software
Version	1.10.1
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
LinkingTo
Suggests	argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub
SystemRequirements
Enhances
URL
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_1.10.1.tar.gz
Windows Binary	Chicago_1.10.1.zip
Mac OS X 10.11 (El Capitan)	Chicago_1.10.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Chicago
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Chicago
Package Short Url	http://bioconductor.org/packages/Chicago/
Package Downloads Report	Download Stats