Type: Package
Package: CellaRepertorium
Title: Methods for clustering and analyzing high-throughput
    single cell immune cell repertoires (RepSeq)
Version: 0.3.2
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"))
Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
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 (>= 3.5.0)
Imports:
    dplyr,
    tibble,
    stringr,
    Biostrings,
    Rcpp,
    reshape2,
    methods,
    rlang,
    purrr,
    Matrix,
    S4Vectors,
    tidyr,
    forcats
Suggests: 
    testthat,
    readr,
    knitr,
    rmarkdown,
    ggplot2,
    BiocStyle,
    ggdendro,
    broom,
    lme4,
    RColorBrewer
LinkingTo: 
    Rcpp
VignetteBuilder: 
    knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
RoxygenNote: 6.1.1
URL: https://github.com/amcdavid/CellaRepertorium
BugReports: https://github.com/amcdavid/CellaRepertorium/issues
Roxygen: list(markdown = TRUE)