immLynx
Linking Advanced TCR Python Pipelines and Hugging Face Models in R
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("immLynx")Details
| Maintainer | Nick Borcherding <ncborch@gmail.com> |
| Author | Nick Borcherding [aut, cre] (ORCID: <https://orcid.org/0000-0003-1427-6342>) |
| License | MIT + file LICENSE |
| URL | https://github.com/BorchLab/immLynx/ |
| Bug Reports | https://github.com/BorchLab/immLynx/issues |
| Source branch | RELEASE_3_23 |
| 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/ |
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 1.0.0, https://bioconductor.org/packages/immLynx.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | immLynx_1.0.0.tar.gz |
| Windows binary (x86_64) | immLynx_1.0.0.zip |
| macOS binary (arm64) | immLynx_1.0.0.tgz |
| macOS binary (x86_64) | immLynx_1.0.0.tgz |
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