VDJ File (required)
Two columns, "id" and "cdr3". "id" column represents ID linking sample data. "cdr3" column represents amino acid sequence of cdr3 region.
Complementarity Scoring
C D G R P K G F
K P D C E G V
Explanation of Files
Antigens File (required)
One or two columns, "antigen" and (optionally) "antigen_sequence". "antigen" column represents hugo symbol of antigen. "antigen_sequence" column, if included, represents amino acid sequence of antigen. If "antigen_sequence" column is not included, wild type sequence wil be found via UNITPROT search.
Survival File (optional)
Three columns, "id", "survival_time", and "survival status". "id" column represents ID linking sample data. "survival_time" column represents time to event/censor (must be numeric). "survival_status" column represents 0 for censor and 1 for event (must be numeric, either 0 or 1). If this file is not iuncluded, no survival analysis will be included in results.
RNA File (optional)
Any number of columns. "id" column represents ID linking sample data. Other columns have hugo symbol in header and represent RNA expression values.
