Chicago

DOI: 10.18129/B9.bioc.Chicago    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see Chicago.

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Bioconductor version: 3.11

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 "4.0") 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, Sequencing, Software
Version 1.16.1
In Bioconductor since BioC 3.3 (R-3.3) (4.5 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_1.16.1.tar.gz
Windows Binary Chicago_1.16.1.zip
macOS 10.13 (High Sierra) Chicago_1.16.1.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 https://bioconductor.org/packages/Chicago/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: