COCOA
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see COCOA.
Coordinate Covariation Analysis
Bioconductor version: 3.10
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>
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")| Introduction to Coordinate Covariation Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, ChIPSeq, DNAMethylation, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GenomeAnnotation, GenomicVariation, ImmunoOncology, MethylSeq, MethylationArray, PrincipalComponent, Sequencing, Software, SystemsBiology |
| Version | 2.0.0 |
| 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, simpleCache, fitdistrplus |
| 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_2.0.0.tar.gz |
| Windows Binary | COCOA_2.0.0.zip |
| Mac OS X 10.11 (El Capitan) | COCOA_2.0.0.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 3.10 | Source Archive |