DESCRIPTION

Package: djvdj
Title: A collection of single-cell V(D)J tools
Version: 0.1.0
Authors@R: c(
    person("Ryan", "Sheridan", , "ryan.sheridan@cuanschutz.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-4012-3147")),
    person("Jay", "Hesselberth", , "jay.hesselberth@gmail.com", role = "ctb"),
    person("Rui", "Fu", , "raysinensis@gmail.com", role = "ctb"),
    person("Kent", "Riemondy", , "kent.riemondy@ucdenver.edu", role = "ctb"),
    person("RNA Bioscience Initiative", role = "fnd")
  )
Description: djvdj provides a single-cell V(D)J analysis workflow that
    integrates with popular single-cell data structures. This includes the
    ability to cluster CDR3 sequences and to quantify repertoire diversity,
    repertoire similarity, and gene segment usage. Tools are also provided to
    generate a variety of visualizations including rarefaction curves, circos
    plots and UMAP projections. 
biocViews: Software, SingleCell, Sequencing, RNASeq
License: MIT + file LICENSE
URL: https://rnabioco.github.io/djvdj/, https://github.com/rnabioco/djvdj/
BugReports: https://github.com/rnabioco/djvdj/issues
Depends:
    R (>= 4.3.0)
Imports: 
    abdiv,
    boot,
    cli,
    ComplexHeatmap,
    dplyr (>= 1.1.1),
    ggplot2 (>= 3.4.0),
    ggrepel,
    ggtrace,
    glue,
    graphics,
    grDevices,
    grid,
    methods,
    purrr,
    readr,
    rlang (>= 0.4.11),
    S4Vectors,
    scales,
    SingleCellExperiment,
    stats,
    stringr,
    tibble,
    tidyr,
    utils
Suggests: 
    Seurat (>= 4.0.0),
    Biostrings,
    circlize,
    covr,
    dbscan,
    edgeR,
    ggseqlogo,
    here,
    igraph (>= 1.3.0),
    iNEXT,
    knitr,
    MASS,
    RColorBrewer,
    rmarkdown,
    roxygen2,
    Rsamtools,
    testthat,
    uwot
VignetteBuilder: 
    knitr
Config/Needs/website: pkgdown, rnabioco/rbitemplate
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3