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
git_url: https://git.bioconductor.org/packages/scRepertoire
git_branch: devel
git_last_commit: 6bb6e79
git_last_commit_date: 2026-06-28
Repository: Bioconductor 3.24
Date/Publication: 2026-06-29
NeedsCompilation: yes
Packaged: 2026-06-30 01:08:38 UTC; biocbuild
Author: Nick Borcherding [aut, cre],
  Qile Yang [aut],
  Ksenia Safina [aut],
  Justin Reimertz [ctb]
Maintainer: Nick Borcherding <ncborch@gmail.com>
