TCR_summary-class       S4 Class for TCR Repertoire Summary
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
summarizeTCRrepertoire
                        Summarize TCR Repertoire Statistics
tokenizeSequences       Tokenize Amino Acid Sequences
validateTCRdata         Validate TCR Data Format
