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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/Chicago.html below:

Bioconductor - Chicago (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews Epigenetics, HiC, Sequencing, Software Version 1.37.1 In Bioconductor since BioC 3.3 (R-3.3) (9 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 See More 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 Package Archives

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

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