COCOA

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

Maintainer: John Lawson <jtl2hk at virginia.edu>

Installation

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

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) (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
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_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
Package Short Url	https://bioconductor.org/packages/COCOA/
Package Downloads Report	Download Stats