immLynx
This is the development version of immLynx; to use it, please install the devel version of Bioconductor.
Linking Advanced TCR Python Pipelines and Hugging Face Models in R
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | Annotation, Classification, Clustering, DimensionReduction, ImmunoOncology, MotifAnnotation, Sequencing, SingleCell, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | immLynx_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | immLynx_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/immLynx |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/immLynx |
| Bioc Package Browser | https://code.bioconductor.org/browse/immLynx/ |
| Package Short Url | https://bioconductor.org/packages/immLynx/ |
| Package Downloads Report | Download Stats |