Package index • tcrdistR

TCRrep Object

S4 class and constructor for TCR repertoire data

Pairwise TCRdist distance calculations

tcrdist_matrix(): Compute pairwise TCRdist distance matrix
tcrdist_rect(): Compute rectangular TCRdist matrix between a query set and a reference set
tcrdist_sparse(): Compute sparse TCRdist matrix as a dgCMatrix
weighted_cdr3_distance(): Weighted CDR3 distance between two CDR3 sequences
bsd4_matrix(): Retrieve the BSD4 substitution matrix
hamming_distance(): Hamming distance between two CDR3 sequences
hamming_matrix(): Pairwise Hamming distance matrix for CDR3 sequences

K-nearest neighbor and radius-based neighbor queries

tcrdist_knn(): K-nearest-neighbors by TCRdist with optional group masking
tcrdist_radius_neighbors(): Radius-based TCRdist neighbor search with optional group masking
knn_from_matrix(): K-nearest-neighbors from a precomputed distance matrix
knn_from_pca(): K-nearest-neighbors from a PCA embedding matrix

TCR clumping detection with background-corrected significance

Match TCRs against literature epitope databases

find_significant_tcrdist_matches(): Find significant TCRdist matches between query and database TCRs
match_tcrs_to_db(): Match TCRs to a literature database
strict_single_chain_match_tcrs_to_db(): Strict CDR3 sequence matching against a database

Kernel PCA and UMAP for TCRdist distance matrices

Logistic regression-based CD8 phenotype scoring

make_cd8_score_table_column(): CD8 logistic regression score for paired TCRs

Repertoire diversity, richness, clonality, and overlap

Hierarchical clustering and neighborhood-based statistics

tcrdist_hclust(): Hierarchical clustering of TCRs by TCRdist
cluster_tcrs(): Cluster TCRs using various algorithms
neighborhood_test(): Test association between a variable and TCR neighborhoods

Quasi-public TCR motif discovery across subjects

Distance-based fuzzy joining of TCR datasets

Plotting functions for TCR repertoire data

plot_tcrdist_heatmap(): Plot a TCRdist pairwise distance heatmap
plot_tcrdist_dendrogram(): Plot a TCRdist-based dendrogram
plot_distance_distribution(): Plot the distribution of pairwise TCRdist distances
plot_cdr3_logo(): Plot a CDR3 sequence logo
plot_cdr3_length(): Plot CDR3 length distribution
plot_junction_bars(): Plot junction bars showing V/N/D/J nucleotide composition
plot_vj_gene_logo(): Plot a V/J gene usage logo
plot_tcr_logo_panel(): Plot a composite TCR rearrangement logo panel
compute_nucseq_src(): Compute nucleotide source annotations for CDR3 sequences
plot_gene_usage(): Plot V-gene or J-gene usage frequencies
plot_tcr_scatter(): Plot a 2D scatter of TCR embeddings
compute_tcr_network(): Build a TCR clone network from distance data
plot_tcr_network(): Plot a TCR clone network

Read and standardize TCR data from various formats

Built-in datasets

Gene database, constants, and helper functions