Chicago
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Chicago.
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
Bioconductor version: 3.9
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>
Citation (from within R, enter
citation("Chicago")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Epigenetics, HiC, ImmunoOncology, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2), data.table |
| Imports | matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub |
| Linking To | |
| Enhances | |
| 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_1.12.0.tar.gz |
| Windows Binary | Chicago_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | Chicago_1.12.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |