DESCRIPTION

Package: scRepertoire
Title: A toolkit for single-cell immune receptor profiling
Version: 2.0.8
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"))
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: 7.3.2
biocViews: Software, ImmunoOncology, SingleCell, Classification, Annotation, Sequencing
Depends: 
     ggplot2, 
     R (>= 4.0)
Imports: 
    assertthat,
    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