Chicago

This is the released version of Chicago; for the devel version, see Chicago.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Bioconductor version: Release (3.23)

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")):

Jonathan Cairns, Paula Freire Pritchett, Steven Wingett, Mikhail Spivakov. Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization. doi:10.18129/B9.bioc.Chicago, R package version 1.40.0, https://bioconductor.org/packages/Chicago.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

CHiCAGO Vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Epigenetics, HiC, Sequencing, Software
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	Artistic-2.0
Depends	R (>= 3.3.1), data.table
Imports	matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils
System Requirements
URL

Suggests	argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub
Linking To
Enhances
Depends On Me	PCHiCdata
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Chicago_1.40.0.tar.gz
Windows Binary (x86_64)	Chicago_1.40.0.zip
macOS Binary (big-sur-x86_64)	Chicago_1.40.0.tgz
macOS Binary (sonoma-arm64)	Chicago_1.40.0.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