Type: Package
Package: CellaRepertorium
Title: Data structures, clustering and testing for single cell immune
        receptor repertoires (scRNAseq RepSeq/AIRR-seq)
Version: 1.8.0
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'
git_url: https://git.bioconductor.org/packages/CellaRepertorium
git_branch: RELEASE_3_16
git_last_commit: 5346a3b
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
Packaged: 2022-11-01 21:05:15 UTC; biocbuild
Author: Andrew McDavid [aut, cre],
  Yu Gu [aut],
  Erik VonKaenel [aut],
  Aaron Wagner [aut],
  Thomas Lin Pedersen [ctb]
Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
