-
Notifications
You must be signed in to change notification settings - Fork 1
TCR generation probabilities #11
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Comments
TCR generation probability: the process of VDJ recombination results in certain CDR3 sequences having a higher probability of occurring. This probability can be computed. Implement module to calculate TCR generation probability for each CDR3 sequence in sample. @yuvalel will advise what software package to use. Related: https://www.pnas.org/doi/pdf/10.1073/pnas.1409572111 |
For TCR generation probability we should use the OLGA package - https://github.com/statbiophys/OLGA |
Input to Olga: vector of CDR3 aa chains for clones in one sample |
There is a very reliable measure of distribution-to-distribution distance, OT (Optimal Transport) aka Wassershtein distance. Having all the pairwise Emerson-to-Emarson sample distances calculated, we can position any new sample relative to Emerson samples looking at its sample-to-Emerson samples distances. |
@KevinMLanderos do you know where the Emerson dataset to test the idea ? |
@dimalvovs I think this is the dataset. n=666 in original cohort and n=120 in independent validation cohort: |
No description provided.
The text was updated successfully, but these errors were encountered: