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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/immLynx/ |
| Package Short Url | https://bioconductor.org/packages/immLynx/ |
| Package Downloads Report | Download Stats |