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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "COCOA" in publications use:'
type: software
license: GPL-3.0-only
title: 'COCOA: Coordinate Covariation Analysis'
version: 2.19.0
doi: 10.1186/s13059-020-02139-4
abstract: 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.
authors:
- family-names: Lawson
  given-names: John
  email: jtl2hk@virginia.edu
- family-names: Sheffield
  given-names: Nathan
  website: http://www.databio.org
preferred-citation:
  type: article
  title: 'COCOA: coordinate covariation analysis of epigenetic heterogeneity'
  authors:
  - family-names: Lawson
    given-names: John T.
  - family-names: Smith
    given-names: Jason P.
  - family-names: Bekiranov
    given-names: Stefan
  - family-names: Garrett-Bakelman
    given-names: Francine E.
  - family-names: Sheffield
    given-names: Nathan C.
  year: '2020'
  journal: Genome Biology
  volume: '21'
  doi: 10.1186/s13059-020-02139-4
  url: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02139-4
repository: https://bioc.r-universe.dev
repository-code: https://github.com/databio/COCOA
url: http://code.databio.org/COCOA/
date-released: '2021-11-18'
contact:
- family-names: Lawson
  given-names: John
  email: jtl2hk@virginia.edu