Linking Advanced TCR Python Pipelines and Hugging Face Models in R

Documentation for package ‘immLynx’ version 1.1.3

convertToTcrdist	Convert TCR Data to tcrdist3 Format
exportToScanpy	Export Single-Cell + Immune Receptor Data to scanpy/scirpy Format
extractTCRdata	Extract TCR Data from SingleCellExperiment Object
generateOLGA	Generate Random TCR Sequences using OLGA
huggingModel	Initialize a Hugging Face Model and Tokenizer
immLynx_example	Example Single-Cell RNA-seq Data with TCR Information
listScXpandModels	List available scXpand pretrained models
proteinEmbeddings	Get Protein Embeddings from a Model
runClustTCR	Run clusTCR Clustering on scRepertoire Data
runDeepTCR	Featurize TCR Sequences with the DeepTCR Variational Autoencoder
runEmbeddings	Generate Protein Language Model Embeddings for TCR Sequences
runHLAassociation	Perform HLA Association Analysis on Metaclones
runMetaclonotypist	Run Metaclonotypist for TCR Metaclone Discovery
runOLGA	Calculate Generation Probability (Pgen) for TCRs in scRepertoire Data
runScXpand	Predict T-cell clonal expansion from gene expression with scXpand
runSoNNia	Run soNNia Selection Analysis
runSymdelNeighbors	Find Near-Neighbor CDR3 Sequences by Symmetric Deletion Lookup
runTCRdist	Calculate TCR Distances on scRepertoire Data
show-method	S4 Class for TCR Repertoire Summary
summarizeTCRrepertoire	Summarize TCR Repertoire Statistics
TCR_summary-class	S4 Class for TCR Repertoire Summary
tokenizeSequences	Tokenize Amino Acid Sequences
validateTCRdata	Validate TCR Data Format