DESCRIPTION

Package: COCOA
Version: 2.4.1
Date: 2020-10-27
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