Package: immLynx
Title: Linking Advanced TCR Python Pipelines and Hugging Face Models in
        R
Version: 1.1.3
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), clonal expansion prediction from
        gene expression (scXpand), near-neighbor search by symmetric
        deletion lookup (pyrepseq), and deep generative featurization
        (DeepTCR). Fully compatible with the scRepertoire and immApex
        ecosystem for single-cell immune repertoire analysis.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: Software, ImmunoOncology, SingleCell, Classification,
        Annotation, Sequencing, MotifAnnotation, Clustering,
        DimensionReduction, GeneExpression
Depends: R (>= 4.5.0)
Imports: basilisk (>= 1.8.0), reticulate (>= 1.24), immApex, methods,
        S4Vectors, SingleCellExperiment, stats, SummarizedExperiment,
        tools, utils, zellkonverter
Suggests: AnnotationDbi, BiocStyle, data.table, ggplot2, knitr,
        markdown, Matrix, org.Hs.eg.db, rmarkdown, scater, scran,
        scRepertoire, Seurat, 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/roxygen2/version: 8.0.0
Config/pak/sysreqs: libicu-dev libpng-dev libxml2-dev libssl-dev
        python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-27 12:29:31 UTC
RemoteUrl: https://github.com/bioc/immLynx
RemoteRef: HEAD
RemoteSha: 0b5b5b44ee5664e888f456b82844767df7930b72
NeedsCompilation: no
Packaged: 2026-10-27 14:54:05 UTC; root
Author: Nick Borcherding [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1427-6342>)
Maintainer: Nick Borcherding <ncborch@gmail.com>