DESCRIPTION

Package: atacr
Type: Package
Title: Analysing Capture Seq Count Data
Version: 0.4.14
Authors@R: c(
  person("Dan","MacLean", email="dan.maclean@tsl.ac.uk", role=c("aut", "cre")),
  person("Ram-Krishna", "Shrestha", email="ram-krishna.shrestha@tsl.ac.uk", role="aut"))
Description: This package helps with the analysis of count data from RNA and ATAC capture-seq experiments.
    Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper
    functions and quality control plots specific to the analysis of particularly windows.
    Especially, atacr is useful for performing control window based between sample normalizations and for
    easily running non-standard tests for differentially accessible windows in common reference designs.
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
LazyData: TRUE
Imports:
    BayesFactor,
    boot,
    biomaRt,
    corrplot,
    csaw,
    dplyr,
    edgeR,
    fitdistrplus,
    GenomeGraphs,
    GenomicAlignments,
    GenomicRanges,
    grid,
    gridExtra,
    ggjoy,
    ggplot2,
    ggthemes,
    heatmap3,
    IRanges,
    magrittr,
    methods,
    plyr,
    RColorBrewer,
    reshape,
    reshape2,
    Rsamtools,
    rtracklayer,
    S4Vectors,
    stringr,
    SummarizedExperiment,
    tidyr
RoxygenNote: 6.0.1
Suggests: testthat,
    knitr,
    pander,
    rmarkdown,
    UpSetR
VignetteBuilder: knitr
biocViews: