immGLIPH/DESCRIPTION at main · BorchLab/immGLIPH · GitHub

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Package: immGLIPH
Title: Grouping of Lymphocyte Interactions by Paratope Hotspots
Version: 0.99.2
Authors@R: c(
    person("Nick", "Borcherding", role = c("aut", "cre"),
           email = "ncborch@gmail.com")
    )
Description: An R implementation of the GLIPH and GLIPH2 algorithms for
    clustering T cell receptors (TCRs) predicted to bind the same
    HLA-restricted peptide antigen. Identifies specificity groups based on
    local (motif-based) and global (sequence-based) CDR3 similarities.
    Integrates with the scRepertoire ecosystem via immApex for single-cell
    immune repertoire analysis. Users should cite the original GLIPH
    algorithm papers: Glanville et al. (2017) <doi:10.1038/nature22976>
    and Huang et al. (2020) <doi:10.1038/s41587-020-0505-4>.
License: MIT + file LICENSE
biocViews:
    Software,
    ImmunoOncology,
    Clustering,
    SingleCell,
    Sequencing,
    Visualization
Depends:
    R (>= 4.5.0)
Imports:
    stringdist,
    igraph,
    foreach,
    doParallel,
    parallel,
    stringr,
    stats,
    utils,
    graphics,
    grDevices,
    viridis,
    visNetwork,
    plotfunctions,
    immApex
Suggests:
    BiocFileCache,
    scRepertoire,
    SeuratObject,
    Seurat,
    SingleCellExperiment,
    testthat (>= 3.0.0),
    BiocStyle,
    knitr,
    rmarkdown
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://github.com/BorchLab/immGLIPH,
    https://github.com/BorchLab/scRepertoire,
    https://github.com/BorchLab/immApex
BugReports: https://github.com/BorchLab/immGLIPH/issues