DESCRIPTION

Package: ALTRE
Type: Package
Title: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data
Version: 0.99.0
Authors@R: c(
 person("Elizabeth", "Baskin", email = "Elizabeth.Baskin@osumc.edu", role = "aut"),
 person("Rick", "Farouni", email = "farouni.1@osu.edu", role = "aut"),
 person("Ewy", "Mathe", email = "Ewy.Mathe@osumc.edu", role = c("aut", "cre")))
Description: This workflow takes alignment data and hotspot calls from assays of
 open chromatin (ATAC-seq, DNase-seq, and FAIRE-seq) and identifies candidate regulatory
 elements (e.g. TSS-distal and TSS-proximal) that differ across cell and tissue type.
URL: https://github.com/Mathelab/ALTRE
BugReports: https://github.com/Mathelab/ALTRE/issues
Depends: R (>= 3.2.0)
Suggests: Rsubread
Imports:
    shiny,
    shinydashboard,
    rmarkdown,
    shinyFiles,
    methods,
    S4Vectors,
    GenomeInfoDb,
    IRanges,
    DESeq2,
    GenomicAlignments,
    SummarizedExperiment,
    GenomicRanges,
    Rsamtools,
    readr,
    org.Hs.eg.db,
    ensembldb,
    AnnotationFilter,
    EnsDb.Hsapiens.v75,
    tidyr,
    dplyr,
    GO.db,
    grid,
    stringr,
    tibble,
    magrittr,
    highcharter,
    htmltools,
    rGREAT,
    RColorBrewer
License: GPL-2
BiocViews: Visualization, Annotation, Software, AnnotationData, FunctionalAnnotation
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no