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] (http://www.databio.org)

Maintainer: John Lawson <jtl2hk at virginia.edu>

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

Installation

To install this package, start R (version "3.6") 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")
COCOA Workflow HTML R Script
Introduction to Coordinate Covariation Analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

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) (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
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
Linking To
Enhances
Depends On Me
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 COCOA_1.2.0.tar.gz
Windows Binary COCOA_1.2.0.zip
Mac OS X 10.11 (El Capitan) COCOA_1.2.0.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
Old Source Packages for BioC 3.9 Source Archive