Package: immLynx Title: Linking Advanced TCR Python Pipelines and Hugging Face Models in R Version: 1.1.0 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.r-universe.dev Date/Publication: 2026-04-28 13:07:11 UTC RemoteUrl: https://github.com/bioc/immLynx RemoteRef: HEAD RemoteSha: f5adcfcc1c2acd3b466125d6ec5651ddecd255f6 NeedsCompilation: no Packaged: 2026-05-30 09:39:57 UTC; root Author: Nick Borcherding [aut, cre] (ORCID: ) Maintainer: Nick Borcherding