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'