DESCRIPTION

Package: HiCAGE
Type: Package
Title: Hi-C Annotation and Graphics Ensemble
Version: 1.0.0
Authors@R: person("Michael", "Workman", email = "michael.workman@cshs.org",
    role = c("aut", "cre"))
Maintainer: Michael Workman <michael.workman@cshs.org>
Description: This package takes chromsome conformation capture data as input
    and annotates each genomic region with segmentation data from StateHub
    (http://statehub.org/statehub/), for example. This data can then be 
    annotated with the nearest gene and using RNA-seq data, expression values 
    can be linked to each gene. Moreover, these data can be combined into a 
    circle plot with heatmaps showing average score of chromsome conformation 
    capture interaction between segmentation marks as well as average FPKM 
    values for genes in each type of interaction.
Depends: R (>= 3.4.1)
Imports: readr,
        tidyr, 
        dplyr,
        GenomicRanges,
        biomaRt,
        IRanges,
        magrittr,
        circlize,
        shiny,
        shinydashboard,
        grDevices, 
        graphics, 
        utils, 
        stats,
        plotrix,
        UpSetR,
        topGO,
        org.Hs.eg.db,
        org.Mm.eg.db
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
biocViews: GeneExpression, GenomeAnnotation, DNA3DStructure, 
    FunctionalPrediction, Visualization, GUI, ChIPSeq, HiC
RoxygenNote: 6.0.1
Suggests: knitr,
    rmarkdown
VignetteBuilder: knitr