Potential Features

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• [ ] 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

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

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

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