immLynx
This is the development version of immLynx; for the stable release version, see immLynx.
All Bioconductor versions of immLynx
3.24 (devel), 3.23 (release)
Linking Advanced TCR Python Pipelines and Hugging Face Models in R
Bioconductor version: 3.24 · Package version: 1.1.0
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.
Author: Nick Borcherding [aut, cre] 
Maintainer: Nick Borcherding <ncborch at gmail.com>
Citation
From within R, enter citation("immLynx"):
Nick Borcherding. immLynx: Linking Advanced TCR Python Pipelines and Hugging Face Models in R. doi:10.18129/B9.bioc.immLynx, R package version 1.1.0, https://bioconductor.org/packages/immLynx.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("immLynx")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/BorchLab/immLynx/ |
| Bug Reports | https://github.com/BorchLab/immLynx/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2322 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Classification, Clustering, DimensionReduction, ImmunoOncology, MotifAnnotation, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/immLynx/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("immLynx")| Advanced TCR Analysis with immLynx | HTML | R Script |
| Getting Started with immLynx | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | immLynx_1.1.0.tar.gz |
| Windows binary (x86_64) | immLynx_1.1.0.zip |
| macOS binary (arm64) | immLynx_1.1.0.tgz |
| macOS binary (x86_64) | immLynx_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/immLynx |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/immLynx |
| Package Downloads Report | Download Stats |
Dependencies
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