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("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 | ||
| 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 |