Package: scRepertoire
Title: A toolkit for single-cell immune receptor profiling
Version: 2.0.0
Authors@R: c(
    person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"), 
    person(given = "Qile", family = "Yang", role = c("aut"), email = "qile0317@gmail.com"), 
    person(given = "Ksenia", family = "Safina", role = c("aut"), email = "safina@broadinstitute.org"))
Description: scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
biocViews: Software, ImmunoOncology, SingleCell, Classification,
        Annotation, Sequencing
Depends: ggplot2, R (>= 4.0)
Imports: cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph,
        grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp,
        reshape2, rjson, rlang, S4Vectors, SeuratObject,
        SingleCellExperiment, stats, stringr, stringdist,
        SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash
Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales,
        scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr
VignetteBuilder: knitr
Config/testthat/edition: 3
Language: en-US
LinkingTo: Rcpp
URL: https://www.borch.dev/uploads/screpertoire/
BugReports: https://github.com/ncborcherding/scRepertoire/issues
git_url: https://git.bioconductor.org/packages/scRepertoire
git_branch: RELEASE_3_19
git_last_commit: 52b5a50
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-04-30
NeedsCompilation: yes
Packaged: 2024-05-01 05:06:33 UTC; biocbuild
Author: Nick Borcherding [aut, cre],
  Qile Yang [aut],
  Ksenia Safina [aut]
Maintainer: Nick Borcherding <ncborch@gmail.com>
Built: R 4.4.0; x86_64-apple-darwin20; 2024-05-01 12:19:59 UTC; unix
