tcrdist_rs documentation

tcrdist_rs is a Rust package with Rust bindings for Python for fast, parallelized CPU TCRdist, hamming, and Levenshtein distance routines, with the latter two based on the triple_accel Rust package. Previous versions of TCRdist have been written in python/numba and C++. All code is freely available at https://github.com/zacmon/tcrdist_rs.

At the moment, all functions associated with tcrdist_allele and tcrdist_gene operate assuming V genes are human V genes. Future work will be done to allow for custom V gene databases.

User Guide

• Installation

API Docmentation

• tcrdist_rs
  • amino_acid_distance()
  • cdr1_distance()
  • cdr2_distance()
  • hamming()
  • hamming_bin_many_to_many()
  • hamming_many_to_many()
  • hamming_matrix()
  • hamming_neighbor_many_to_many()
  • hamming_neighbor_matrix()
  • hamming_neighbor_one_to_many()
  • hamming_neighbor_pairwise()
  • hamming_one_to_many()
  • hamming_pairwise()
  • levenshtein()
  • levenshtein_bin_many_to_many()
  • levenshtein_exp()
  • levenshtein_exp_bin_many_to_many()
  • levenshtein_exp_many_to_many()
  • levenshtein_exp_matrix()
  • levenshtein_exp_neighbor_many_to_many()
  • levenshtein_exp_neighbor_matrix()
  • levenshtein_exp_neighbor_one_to_many()
  • levenshtein_exp_neighbor_pairwise()
  • levenshtein_exp_one_to_many()
  • levenshtein_exp_pairwise()
  • levenshtein_many_to_many()
  • levenshtein_matrix()
  • levenshtein_neighbor_many_to_many()
  • levenshtein_neighbor_matrix()
  • levenshtein_neighbor_one_to_many()
  • levenshtein_neighbor_pairwise()
  • levenshtein_one_to_many()
  • levenshtein_pairwise()
  • phmc_distance()
  • tcrdist()
  • tcrdist_allele()
  • tcrdist_allele_many_to_many()
  • tcrdist_allele_matrix()
  • tcrdist_allele_one_to_many()
  • tcrdist_allele_pairwise()
  • tcrdist_gene()
  • tcrdist_gene_many_to_many()
  • tcrdist_gene_matrix()
  • tcrdist_gene_neighbor()
  • tcrdist_gene_neighbor_many_to_many()
  • tcrdist_gene_neighbor_matrix()
  • tcrdist_gene_neighbor_one_to_many()
  • tcrdist_gene_neighbor_pairwise()
  • tcrdist_gene_one_to_many()
  • tcrdist_gene_pairwise()
  • tcrdist_many_to_many()
  • tcrdist_matrix()
  • tcrdist_neighbor_many_to_many()
  • tcrdist_neighbor_matrix()
  • tcrdist_neighbor_one_to_many()
  • tcrdist_neighbor_pairwise()
  • tcrdist_one_to_many()
  • tcrdist_paired_gene()
  • tcrdist_paired_gene_many_to_many()
  • tcrdist_paired_gene_matrix()
  • tcrdist_paired_gene_neighbor_many_to_many()
  • tcrdist_paired_gene_neighbor_matrix()
  • tcrdist_paired_gene_neighbor_one_to_many()
  • tcrdist_paired_gene_neighbor_pairwise()
  • tcrdist_paired_gene_one_to_many()
  • tcrdist_paired_gene_pairwise()
  • tcrdist_pairwise()
  • v_total_distance()
  • version()

Developer Documentation

• Developer tools
• To-do list

References

• Dash et al. (2017) “Quantifiable predictive features define epitope-specific T cell receptor repertoires.” Nature 547(89-93). https://doi.org/10.1038/nature22383

• Mayer-Blackwell et al. (2021) “TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs.” eLife 10:68605. https://doi.org/10.7554/eLife.68605

Indices and tables

• Index

• Module Index

• Search Page