Package: COCOA
Version: 1.0.1
Date: 2018-10-29
Title: Coordinate Covariation Analysis
Description: 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.
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"))
Depends: R (>= 3.5), GenomicRanges
Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2,
        Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid,
        grDevices
Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown,
        AnnotationHub, LOLA
VignetteBuilder: knitr
License: GPL-3
biocViews: PrincipalComponent, GenomicVariation, DNAMethylation,
        GeneRegulation, GenomeAnnotation, SystemsBiology,
        FunctionalGenomics, ChIPSeq, MethylSeq, Sequencing,
        Epigenetics, ImmunoOncology
URL: http://code.databio.org/COCOA/
BugReports: https://github.com/databio/COCOA
RoxygenNote: 6.1.0
git_url: https://git.bioconductor.org/packages/COCOA
git_branch: RELEASE_3_8
git_last_commit: bd6d6de
git_last_commit_date: 2018-12-05
Date/Publication: 2018-12-05
NeedsCompilation: no
Packaged: 2018-12-06 03:22:35 UTC; biocbuild
Author: John Lawson [aut, cre],
  Nathan Sheffield [aut] (http://www.databio.org)
Maintainer: John Lawson <jtl2hk@virginia.edu>
Built: R 3.5.1; ; 2018-12-21 22:11:30 UTC; unix
