Introduction | Setup | Comparing Clustering Methods | Custom Embedding Workflows | Using Different ESM-2 Model Sizes | Embedding Both Chains | Integration with scRepertoire Clonotypes | Analyzing Selection Pressure | Combining Distance-Based Methods | Working with Large Datasets | HLA Association Analysis | Exporting Results | Best Practices | Session Info
Package: immLynx 1.1.0
Nick Borcherding
immLynx: Linking Advanced TCR Python Pipelines and Hugging Face Models in R
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.
Authors:
immLynx_1.1.0.tar.gz
immLynx_1.1.0.zip(r-4.7)immLynx_1.1.0.zip(r-4.6)immLynx_1.1.0.zip(r-4.5)
immLynx_1.1.0.tar.gz(r-4.7-any)immLynx_1.1.0.tar.gz(r-4.6-any)
immLynx_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
immLynx/json (API)
| # Install 'immLynx' in R: |
| install.packages('immLynx', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/borchlab/immlynx/issues
Datasets:
- immLynx_example - Example Single-Cell RNA-seq Data with TCR Information
On BioConductor:immLynx-1.1.0(bioc 3.24)immLynx-1.0.0(bioc 3.23)
softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotationclusteringdimensionreduction
Last updated from:f5adcfcc1c. Checks:6 NOTE, 2 OK, 2 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 176 | ||
| linux-devel-x86_64 | NOTE | 1111 | ||
| source / vignettes | OK | 277 | ||
| linux-release-x86_64 | NOTE | 1122 | ||
| macos-release-arm64 | FAIL | 3710 | ||
| macos-oldrel-arm64 | FAIL | 3688 | ||
| windows-devel | NOTE | 834 | ||
| windows-release | NOTE | 841 | ||
| windows-oldrel | NOTE | 873 | ||
| wasm-release | OK | 176 |
Exports:convertToTcrdistextractTCRdatagenerateOLGAhuggingModelproteinEmbeddingsrunClustTCRrunEmbeddingsrunHLAassociationrunMetaclonotypistrunOLGArunSoNNiarunTCRdistshowsummarizeTCRrepertoiretokenizeSequencesvalidateTCRdata
Dependencies:abindaskpassbasiliskBiobaseBiocGenericsBiostringsclicrayoncurlDelayedArraydir.expiryfilelockgenericsGenomicRangesglueherehttrimmApeximmReferentIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngR6rappdirsRcppRcppTOMLreticulaterlangrprojrootrvestS4ArraysS4VectorsselectrSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbleutf8vctrswithrxml2XVectoryaml
Advanced TCR Analysis with immLynx
Last update: 2026-04-16
Started: 2026-01-04
Getting Started with immLynx
Introduction | Installation | Python Dependencies | Quick Start | Loading the Package and Example Data | Extracting TCR Data | Summarizing TCR Repertoire | Analysis Functions | TCR Clustering with clusTCR | TCR Distance Calculations with tcrdist3 | Generation Probability with OLGA | Protein Language Model Embeddings | Metaclone Discovery with Metaclonotypist | Selection Inference with soNNia | Workflow Example | Session Info
Last update: 2026-04-16
Started: 2026-01-04
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert TCR Data to tcrdist3 Format | convertToTcrdist |
| Extract TCR Data from SingleCellExperiment Object | extractTCRdata |
| Generate Random TCR Sequences using OLGA | generateOLGA |
| Initialize a Hugging Face Model and Tokenizer | huggingModel |
| Example Single-Cell RNA-seq Data with TCR Information | immLynx_example |
| Get Protein Embeddings from a Model | proteinEmbeddings |
| Run clusTCR Clustering on scRepertoire Data | runClustTCR |
| Generate Protein Language Model Embeddings for TCR Sequences | runEmbeddings |
| Perform HLA Association Analysis on Metaclones | runHLAassociation |
| Run Metaclonotypist for TCR Metaclone Discovery | runMetaclonotypist |
| Calculate Generation Probability (Pgen) for TCRs in scRepertoire Data | runOLGA |
| Run soNNia Selection Analysis | runSoNNia |
| Calculate TCR Distances on scRepertoire Data | runTCRdist |
| Summarize TCR Repertoire Statistics | summarizeTCRrepertoire |
| S4 Class for TCR Repertoire Summary | show,TCR_summary-method TCR_summary-class |
| Tokenize Amino Acid Sequences | tokenizeSequences |
| Validate TCR Data Format | validateTCRdata |
