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Published 20 hours ago • verified publisher icon rnabioco

Potential Features

Open sheridar opened this issue 5 years ago • 3 comments

  • [ ] Antigen affinity score
    • Incorporates AVID-seq counts and total receptor counts (CITE-seq/GEX counts)
  • [x] Add VDJ data from cellranger to Seurat object
  • [x] Receptor diversity
    • inverse Simpson index
  • [x] Repertoire overlap
    • Jaccard index
    • Morisita-Horn Index
  • [x] Cluster based on BCR sequence
    • wrapper for enclone
  • [x] Plotting functions
    • Rarefaction curves

sheridar avatar Mar 25 '20 17:03 sheridar

Some existing tools for BCR/TCR analysis: https://immcantation.readthedocs.io/en/stable/

sheridar avatar Sep 03 '20 01:09 sheridar

Some other tools for population diversity/similarity: https://www.rdocumentation.org/packages/divo/versions/1.0.1 https://github.com/kylebittinger/abdiv

sheridar avatar Oct 16 '20 15:10 sheridar

A VDJ package that integrates with scanpy: https://icbi-lab.github.io/scirpy/index.html

sheridar avatar Nov 11 '20 17:11 sheridar