obrzts/BLscore: Clustering Similar TCRs Likely Recognizing Same Epitope

BLscore provides functions to identify clusters of convergent TCRs that are likely to recognize the same peptide. The clustering is based on pairwise comparisons of all TCRs by aligning their CDR1-3 and calculating the alignment scores using BLOSUM62 substitution matrix reflecting evolutionary amino acid interchangeability. The three alignment scores (CDR1, CDR2 and CDR3) are logistically transformed into a single score (BL-score, BLOSUM-logistic) ranging from 0 to 1, where 1 corresponds to the highest probability of specificity match and 0 to the lowest. Because the CDRs differ in their impact on TCR specificity, they are weighted differently in the logistic function. The weights and clustering thresholds were established using available data sets of TCRs with known specificity (VDJdb and IEDB).

install.packages("remotes")
remotes::install_github("obrzts/BLscore")