COCOA

DOI: 10.18129/B9.bioc.COCOA    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see COCOA.

Coordinate Covariation Analysis

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Introduction to Coordinate Covariation Analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, ChIPSeq, DNAMethylation, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, GenomicVariation, ImmunoOncology, MethylSeq, MethylationArray, PrincipalComponent, Sequencing, Software, SystemsBiology
Version	2.4.0
In Bioconductor since	BioC 3.8 (R-3.5) (2.5 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
LinkingTo
Suggests	knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
SystemRequirements
Enhances
URL	http://code.databio.org/COCOA/
BugReports	https://github.com/databio/COCOA
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	COCOA_2.4.0.tar.gz
Windows Binary	COCOA_2.4.0.zip
macOS 10.13 (High Sierra)	COCOA_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/COCOA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/COCOA
Package Short Url	https://bioconductor.org/packages/COCOA/
Package Downloads Report	Download Stats