scirpy icon indicating copy to clipboard operation
scirpy copied to clipboard

Add more epitope databases to `datasets`

Open grst opened this issue 2 years ago • 3 comments

List adapted from #54.

  • [ ] The MAIT reference database with invariant CDR3
  • [ ] huARdb https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab857/6381136?rss=1
  • [ ] McPAS-TCR
  • [ ] PIRD
  • [ ] The Adaptive Biotechnology database, used to identify (and exclude) public clonotypes shared between unrelated individuals (Dean et al., 2015)
  • [ ] There might be quite some SARS-COV-2 TCR-epitope resources as well (e.g., Grifoni et al. 2021)
  • [x] VDJDB
  • [x] IEDB

grst avatar Nov 15 '21 20:11 grst

@ausserh, how about adding your code for IEDB to scirpy directly?

grst avatar Jun 23 '22 14:06 grst

More databases can potentially be accessed via biocypher. See also #404. CC @slobentanzer

grst avatar May 23 '23 15:05 grst

am on holiday, but will address this once i am back. mcpas is included in the adapters we did at the hackathon. cc @dbdimitrov

slobentanzer avatar May 23 '23 16:05 slobentanzer