Package: scRepertoire
Title: A toolkit for single-cell immune receptor profiling
Version: 2.9.1
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 = "qile.yang@berkeley.edu"), 
    person(given = "Ksenia", family = "Safina", role = c("aut"), email = "safina@broadinstitute.org"),
    person(given = "Justin", family = "Reimertz", role = c("ctb"), email = "justin.reimertz@childrens.harvard.edu"))
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,
        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 single-cell
        workflows.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews: Software, ImmunoOncology, SingleCell, Classification,
        Annotation, Sequencing
Depends: ggplot2, R (>= 4.0)
Imports: BiocParallel, dplyr, evmix, ggalluvial, ggdendro, ggraph,
        grDevices, igraph, immApex (>= 1.7.1), iNEXT, Matrix, quantreg,
        Rcpp, rjson, rlang, S4Vectors, SeuratObject,
        SingleCellExperiment, SummarizedExperiment, tidygraph, purrr,
        lifecycle, methods
Suggests: BiocManager, BiocStyle, circlize, dowser, knitr, Peptides,
        rmarkdown, scales, scater, Seurat, spelling, testthat (>=
        3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Language: en-US
LinkingTo: Rcpp
URL: https://www.borch.dev/uploads/scRepertoire/
BugReports: https://github.com/BorchLab/scRepertoire/issues
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        libgsl0-dev libicu-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-28 19:30:57 UTC
RemoteUrl: https://github.com/bioc/scRepertoire
RemoteRef: HEAD
RemoteSha: 6bb6e79f7ae7d17bcd9790292b328f3bd426106e
NeedsCompilation: yes
Packaged: 2026-06-28 22:12:09 UTC; root
Author: Nick Borcherding [aut, cre],
  Qile Yang [aut],
  Ksenia Safina [aut],
  Justin Reimertz [ctb]
Maintainer: Nick Borcherding <ncborch@gmail.com>
Built: R 4.6.1; x86_64-w64-mingw32; 2026-06-28 22:21:43 UTC; windows
Archs: x64
