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Potential Features #1

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5 of 6 tasks

sheridar opened this issue Mar 25, 2020 · 3 comments

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sheridar commented Mar 25, 2020 •

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

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sheridar commented Sep 3, 2020

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

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sheridar commented Oct 16, 2020 •

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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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sheridar commented Nov 11, 2020

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

sheridar added the enhancement label

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