Type: Package
Package: CellaRepertorium
Title: Data structures, clustering and testing for single 
    cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
Version: 1.9.0
Authors@R: 
    c(person(given = "Andrew",
             family = "McDavid",
             role = c('aut', 'cre'),
             email = "Andrew_McDavid@urmc.rochester.edu"),
      person(given = "Yu",
             family = "Gu",
             role = "aut",
             email = "Yu_Gu@urmc.rochester.edu"),
      person(given = 'Erik',
      family = 'VonKaenel',
      role = 'aut'
      ),
      person(given = 'Aaron',
      family = 'Wagner',
      role = 'aut'),
      person(given = 'Thomas Lin',
             family = 'Pedersen', 
             role = 'ctb'))
Description: Methods to cluster and analyze high-throughput
    single cell immune cell repertoires, especially from the 10X Genomics
    VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006).   
    Methods to visualize and analyze paired heavy-light chain data.
    Tests for specific expansion, as well as omnibus oligoclonality under
    hypergeometric models.
License: GPL-3
Depends: 
    R (>= 4.0)
Imports:
    dplyr,
    tibble,
    stringr,
    Biostrings,
    Rcpp,
    reshape2,
    methods,
    rlang (>= 0.3),
    purrr,
    Matrix,
    S4Vectors,
    BiocGenerics,
    tidyr,
    forcats,
    progress,
    stats,
    utils,
    generics,
    glue
Suggests: 
    testthat,
    readr,
    knitr,
    rmarkdown,
    ggplot2,
    BiocStyle,
    ggdendro,
    broom,
    lme4,
    RColorBrewer,
    SingleCellExperiment,
    scater,
    broom.mixed,
    cowplot,
    igraph,
    ggraph
LinkingTo: 
    Rcpp
VignetteBuilder: 
    knitr
Encoding: UTF-8
NeedsCompilation: yes
RoxygenNote: 7.1.2
URL: https://github.com/amcdavid/CellaRepertorium
BugReports: https://github.com/amcdavid/CellaRepertorium/issues
Roxygen: list(markdown = TRUE)
biocViews: RNASeq, Transcriptomics, SingleCell, TargetedResequencing, 
    Technology, ImmunoOncology, Clustering
Collate: 
    'AllClasses.R'
    'ContigCellDB-methods.R'
    'RcppExports.R'
    'auxiliary.R'
    'ccdb_join.R'
    'cdhit-methods.R'
    'cluster-testing.R'
    'clustering-methods.R'
    'data.R'
    'ggplot2-utils.R'
    'pairing-methods.R'
    'reexports.R'
    'permutation-testing.R'
    'plot_clustering.R'
    'plotting.R'
    'pseudo-bulk.R'
    'utilty.R'
    'vdjcellranger-methods.R'