Package: immLynx 1.1.3

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), clonal expansion prediction from gene expression (scXpand), near-neighbor search by symmetric deletion lookup (pyrepseq), and deep generative featurization (DeepTCR). Fully compatible with the scRepertoire and immApex ecosystem for single-cell immune repertoire analysis.

Authors:Nick Borcherding [aut, cre]

immLynx_1.1.3.tar.gz
immLynx_1.1.3.zip(r-4.7-any)immLynx_1.1.3.zip(r-4.6-any)immLynx_1.1.3.zip(r-4.5-any)
immLynx_1.1.3.tar.gz(r-4.7-any)immLynx_1.1.3.tar.gz(r-4.6-any)
immLynx_1.1.3.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:

On BioConductor:immLynx-1.1.0(bioc 3.24)immLynx-1.0.0(bioc 3.23)

softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotationclusteringdimensionreductiongeneexpression

5.71 score 3 stars 6 scripts 364 downloads 21 exports 58 dependencies

Last updated from:0b5b5b44ee. Checks:4 NOTE, 2 ERROR, 2 OK, 2 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE345
linux-develERROR850
source / vignettesOK569
linux-releaseERROR943
macos-releaseFAIL3738
macos-oldrelFAIL593
windows-develNOTE1589
windows-releaseNOTE1286
windows-oldrelNOTE1528
wasm-releaseOK314

Exports:convertToTcrdistexportToScanpyextractTCRdatagenerateOLGAhuggingModellistScXpandModelsproteinEmbeddingsrunClustTCRrunDeepTCRrunEmbeddingsrunHLAassociationrunMetaclonotypistrunOLGArunScXpandrunSoNNiarunSymdelNeighborsrunTCRdistshowsummarizeTCRrepertoiretokenizeSequencesvalidateTCRdata

Dependencies:abindaskpassbasiliskBiobaseBiocGenericsBiostringsclicrayoncurlDelayedArraydir.expiryfilelockgenericsGenomicRangesglueherehttrimmApeximmReferentIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngR6rappdirsRcppRcppTOMLreticulaterlangrprojrootrvestS4ArraysS4VectorsselectrSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbleutf8vctrswithrxml2XVectoryamlzellkonverter

Advanced TCR Analysis with immLynx
Introduction | Setup | Comparing Clustering Methods | Custom Embedding Workflows | Using Different ESM-2 Model Sizes | Embedding Both Chains | Dataset-Specific Features with DeepTCR | Integration with scRepertoire Clonotypes | Predicting Clonal Expansion from Gene Expression | Benchmarking against the observed repertoire | Analyzing Selection Pressure | Combining Distance-Based Methods | Working with Large Datasets | HLA Association Analysis | Exporting Results | Best Practices | Session Info
Rendered fromadvanced_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-10-16
Started: 2026-01-04

Getting Started with immLynx
Introduction | Citation | Installation | Python Dependencies | Quick Start | Loading the Package and Example Data | Extracting TCR Data | Summarizing TCR Repertoire | Analysis Functions | TCR Clustering with clusTCR | Near-Neighbor Search with symdel | TCR Distance Calculations with tcrdist3 | Generation Probability with OLGA | Protein Language Model Embeddings | Deep Generative Featurization with DeepTCR | Metaclone Discovery with Metaclonotypist | Selection Inference with soNNia | Workflow Example | Handing Off to Python: scanpy and scirpy | Session Info
Rendered fromimmLynx_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-10-16
Started: 2026-01-04