I am working with a dataset that includes CDR3 amino acid sequences from TCR-seq, epitopes, HLA-type, gene expression (from RNA-seq), and species information. My goal is to understand how antigen-specific TCRs interact with these epitopes and analyze the functional response of these T cells by linking them to gene expression profiles. I would appreciate insights on methods to integrate RNA-seq and TCR-seq data for studying antigen-specific TCR interactions.

Thank you