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COCOA

Coordinate Covariation Analysis


Bioconductor version: Release (3.18)

COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.

Author: John Lawson [aut, cre], Nathan Sheffield [aut] (http://www.databio.org), Jason Smith [ctb]

Maintainer: John Lawson <jtl2hk at virginia.edu>

Citation (from within R, enter citation("COCOA")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("COCOA")

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("COCOA")
Introduction to Coordinate Covariation Analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, ChIPSeq, DNAMethylation, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, GenomicVariation, ImmunoOncology, MethylSeq, MethylationArray, PrincipalComponent, Sequencing, Software, SystemsBiology
Version 2.16.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges
Imports BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus
System Requirements
URL http://code.databio.org/COCOA/
Bug Reports https://github.com/databio/COCOA
See More
Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
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Package Archives

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

Source Package COCOA_2.16.0.tar.gz
Windows Binary COCOA_2.16.0.zip
macOS Binary (x86_64) COCOA_2.16.0.tgz
macOS Binary (arm64) COCOA_2.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/COCOA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/COCOA
Bioc Package Browser https://code.bioconductor.org/browse/COCOA/
Package Short Url https://bioconductor.org/packages/COCOA/
Package Downloads Report Download Stats