Jamie Heather

Any way/plans to include information about a *lack* of antigen association?

1

I'm curious about whether there is/should be a way for people to report the lack of a specific TCR-pMHC interaction. Obviously sometimes this will occur within the bounds of a...

Currently when submitting a rearrangements using nucleotide CDR3s, Stitchr will produce a small proportion of TCRs where the stitched nucleotide sequence does not exactly replicate the sequence that appeared in...

Currently `stitchr` uses Kasuza frequency data to pick codons for residues that are not wholly germline-encodable when providing AA CDRs. This basically picks the most common nucleotide triplet used from...

Currently it's awkward to add additional genes, both due to having to confirm to the altered IMGT header format and locating the relevant file in the squirreled away data directory....

Using 'TRAVx*%' in Thimble _should_ produce rows in the output for that rearrangement with all included alleles of TRAVx, however it currently only includes alleles that are included in the...

**The issue** IGoR seems to be routinely over-estimating the number of TRAV/TRBV gene deletions (and therefore presumably is correspondingly doing less well in other parameters too). **Additional context** When running...

`antigen.gene` / `antigen.species` mix up for some human epitopes

1

I've just updated an analysis to use the May 2024 release and noticed that there's a few entries for anti-human TCRs that appear to have the `antigen.gene` and `antigen.species` fields...