Package: immGLIPH
Title: Grouping of Lymphocyte Interactions by Paratope Hotspots
Version: 0.99.5
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
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-20 12:06:01 UTC
RemoteUrl: https://github.com/bioc/immGLIPH
RemoteRef: HEAD
RemoteSha: 17636de1dcad06e64a93a739d88bf90eb2d41c83
NeedsCompilation: no
Packaged: 2026-07-08 08:40:04 UTC; root
Author: Nick Borcherding [aut, cre]
Maintainer: Nick Borcherding <ncborch@gmail.com>