Package: immLynx
Title: Linking Advanced TCR Python Pipelines and Hugging Face Models in
        R
Version: 1.0.0
Authors@R: c(
    person(given = "Nick", family = "Borcherding", role = c("aut", "cre"),
           email = "ncborch@gmail.com",
           comment = c(ORCID = "0000-0003-1427-6342")))
Description: A comprehensive toolkit that bridges popular Python-based
        immune repertoire analysis tools and Hugging Face protein
        language models into the R environment. Provides unified
        interfaces for TCR distance calculations (tcrdist3), sequence
        generation probability (OLGA), selection inference (soNNia),
        clustering (clusTCR), protein embeddings (ESM-2), metaclone
        discovery (metaclonotypist). Fully compatible with the
        scRepertoire and immApex ecosystem for single-cell immune
        repertoire analysis.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
biocViews: Software, ImmunoOncology, SingleCell, Classification,
        Annotation, Sequencing, MotifAnnotation, Clustering,
        DimensionReduction
Depends: R (>= 4.5.0)
Imports: basilisk (>= 1.8.0), reticulate (>= 1.24), immApex, methods,
        S4Vectors, SingleCellExperiment, stats, SummarizedExperiment,
        utils
Suggests: BiocStyle, ggplot2, knitr, markdown, rmarkdown, scater,
        scran, scRepertoire, spelling, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
Language: en-US
URL: https://github.com/BorchLab/immLynx/
BugReports: https://github.com/BorchLab/immLynx/issues
StagedInstall: no
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev libpng-dev libxml2-dev libssl-dev
        python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:07:11 UTC
RemoteUrl: https://github.com/bioc/immLynx
RemoteRef: RELEASE_3_23
RemoteSha: e2fd5794bff0b71d8be08f0154e75395c2262b4a
NeedsCompilation: no
Packaged: 2026-04-29 22:24:49 UTC; root
Author: Nick Borcherding [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1427-6342>)
Maintainer: Nick Borcherding <ncborch@gmail.com>
Built: R 4.6.0; ; 2026-04-29 22:27:24 UTC; windows
