DOI: 10.18129/B9.bioc.COCOA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see COCOA.

Coordinate Covariation Analysis

Bioconductor version: 3.9

COCOA is a method for understanding variation among samples and can be used with data that includes genomic coordinates such as DNA methylation. On a high level, COCOA uses a database of "region sets" and principal component analysis (PCA) of your data to identify sources of variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance, transcription factor binding regions, histone modification regions, or open chromatin regions. COCOA works in both supervised (known groups of samples) and unsupervised (no groups) situations and can be used as a complement to "differential" methods that find discrete differences between groups. COCOA can identify biologically meaningful sources of variation between samples and increase understanding of variation in your data.

Author: John Lawson [aut, cre], Nathan Sheffield [aut] (

Maintainer: John Lawson <jtl2hk at>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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


biocViews ChIPSeq, DNAMethylation, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, GenomicVariation, ImmunoOncology, MethylSeq, PrincipalComponent, Sequencing, Software, SystemsBiology
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
License GPL-3
Depends R (>= 3.5), GenomicRanges
Imports BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices
Suggests knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA
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_1.2.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) COCOA_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: