Package: immGLIPH
Title: Grouping of Lymphocyte Interactions by Paratope Hotspots
Version: 0.99.4
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, BiocParallel, 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
NeedsCompilation: no
Packaged: 2026-05-03 11:13:36 UTC; pkgbuild
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch@gmail.com>
