immLynx
This is the released version of immLynx; for the devel version, see immLynx.
Linking Advanced TCR Python Pipelines and Hugging Face Models in R
Bioconductor version: Release (3.23)
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("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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("immLynx")For older versions of R, please refer to the appropriate Bioconductor release.
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 | |
| LICENSE | Text |
Details
| biocViews | Annotation, Classification, Clustering, DimensionReduction, ImmunoOncology, MotifAnnotation, Sequencing, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | basilisk (>= 1.8.0), reticulate (>= 1.24), immApex, methods, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/BorchLab/immLynx/ |
| Bug Reports | https://github.com/BorchLab/immLynx/issues |
See More
| Suggests | BiocStyle, ggplot2, knitr, markdown, rmarkdown, scater, scran, scRepertoire, spelling, testthat (>= 3.0.0), withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | immLynx_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | immLynx_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/immLynx |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/immLynx |
| Package Short Url | https://bioconductor.org/packages/immLynx/ |
| Package Downloads Report | Download Stats |