Package: COCOA
Version: 2.25.0
Date: 2025-06-25
Title: Coordinate Covariation Analysis
Description: 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@R: c(person("John", "Lawson", email="jtl2hk@virginia.edu", role=c("aut", "cre")), person("Nathan", "Sheffield", role=c("aut"), comment="http://www.databio.org"), person("Jason", "Smith", role=c("ctb")))
Depends: R (>= 3.5), GenomicRanges
Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2,
        Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid,
        grDevices, simpleCache, fitdistrplus
Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown,
        AnnotationHub, LOLA
VignetteBuilder: knitr
License: GPL-3
biocViews: Epigenetics, DNAMethylation, ATACSeq, DNaseSeq, MethylSeq,
        MethylationArray, PrincipalComponent, GenomicVariation,
        GeneRegulation, GenomeAnnotation, SystemsBiology,
        FunctionalGenomics, ChIPSeq, Sequencing, ImmunoOncology
URL: http://code.databio.org/COCOA/
BugReports: https://github.com/databio/COCOA
RoxygenNote: 7.1.1
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:48:30 UTC
RemoteUrl: https://github.com/bioc/COCOA
RemoteRef: HEAD
RemoteSha: a245a29ef8f4f7c38b64886d3ac9f1b8092ddd3c
NeedsCompilation: no
Packaged: 2026-01-09 21:11:05 UTC; root
Author: John Lawson [aut, cre],
  Nathan Sheffield [aut] (http://www.databio.org),
  Jason Smith [ctb]
Maintainer: John Lawson <jtl2hk@virginia.edu>
Built: R 4.6.0; ; 2026-01-09 21:13:30 UTC; windows
