DESCRIPTION

Package: copykit
Title: CopyKit
URL: https://github.com/navinlabcode/copykit
BugReports: https://github.com/navinlabcode/copykit/issues
Version: 0.1.3
Authors@R: c(
    person(given = "Darlan",
           family = "Conterno Minussi",
           role = c("aut", "cre"),
           email = "dcminussi@mdanderson.org",
           comment = c(ORCID = "0000-0001-8856-4625")),
               person(given = "Junke",
           family = "Wang",
           role = c("ctb"),
           email = "JWang48@mdanderson.org",
           comment = c(ORCID = "0000-0002-3733-5192")),
    person(given = "Yun",
           family = "Yan",
           role = c("ctb"),
           email = "yun.yan@uth.tmc.edu",
           comment = c(ORCID = "0000-0002-3701-9608")) )
Description: A suite of tools for single cell copy number analysis 
        focusing on reads binning, segmentation, normalization, 
        filtering, analysis, and visualization. CopyKit extends Bioconductors’ 
        SingleCellExperiment class for the analysis of copy number datasets.
        We divide CopyKit functions into four modules: 1) Pre-processing,
        2) Quality Control, 3) Data Analysis, and 4) Visualization. CopyKit
        can be applied to a broad applications for studying diverse areas of 
        cancer biology, including intratumor heterogeneity, premalignant 
        progression, and metastasis. 
License: AGPL (>= 3) + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: 
    testthat,
    spelling,
    knitr,
    rmarkdown,
    stringr
Language: en-US
biocViews: Software, SingleCell, DNASeq, Sequencing, 
           Visualization, Normalization, Clustering,
           ImmunoOncology, DataImport, CellBiology, QualityControl
Imports: 
    dplyr,
    uwot,
    ggplot2,
    grDevices,
    magrittr,
    SummarizedExperiment,
    ComplexHeatmap,
    fastcluster,
    amap,
    ape,
    S4Vectors,
    scales,
    shiny,
    miniUI,
    tidyr,
    igraph (>= 1.2.8),
    BiocGenerics,
    grid,
    ggbeeswarm,
    dbscan,
    mixtools,
    stats,
    gtools,
    forcats,
    circlize,
    BiocParallel,
    fpc,
    ggnewscale,
    ggalluvial,
    viridis,
    ggtree,
    methods,
    withr,
    bluster,
    scquantum
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Depends: 
    SingleCellExperiment,
    R (>= 4.0.0),
    Rsubread,
    GenomicRanges,
    DNAcopy