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Uses: #200 #201 #202 #117
Immune receptor interactions with epitopes for use in single cell analyses.
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Thank you very much for your amazing project! We have a few questions from our attempts running this model.
[1] We observed some interesting patterns when running tcr-esm. More specifically, we gen…
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Hi Zhenghong,
Thanks for providing a useful tool, I have another usage question.
A generation example has been provided in the readme,
```
python GRA.py --data_path='./Data/MIRA/MIRA.csv' --tc…
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HI,
I found your paper to be very interesting. I would like to use the pipeline you developed to screen for high-affinity epitopes using training-validated known epitope data based on the CDR3 sequ…
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Thank you for such a nice tool! I would like to ask 1) whether the zero-shot (TCR and epitope) datasets are available and 2) whether the zero-shot setting concern both unseen epitope and unseen TCR si…
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Hello, I have two questions to ask you. First, are the model training sets and test sets from VDJdb? What are the filtering conditions?
Second, if I want to use your model directly to predict which e…
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This would be one way to integrate consideration of TCR repertoire data. If a user has TCR data from TILs say, they could use TCRMatch to further prioritize candidates where TCRMatch reports a hit in…
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Hello again!
I want to process the sequencing data obtained by Croce _et al_ in **"Phage display profiling of CDR3β loops enables machine learning predictions of NY-ESO-1 specific TCRs"** with TRUS…
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[Connelley TK, MacHugh ND, Pelle R, Weir W, Morrison WI. Escape from CD8+ T cell response by natural variants of an immunodominant epitope from Theileria parva is predominantly due to loss of TCR reco…
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Every epitope should be annotated with its nearest neighbor(s) in the reference proteome and the edit distance to those sequences. The edit function should only allow substitutions but not insertions …