Ryan Sheridan
Ryan Sheridan
I like the PCA idea, here's an example of a heatmap: https://github.com/rnabioco/antigen-tracking/commit/5d2251b922a497dd25af85d0df3fc9e047edcfaf
see #126 and #127
I'll downsample the current vignette data so we can include it in the package
Thymic development TCR: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8581/samples/?s_page=1&s_pagesize=500 COVID19 TCR/BCR: https://www.nature.com/articles/s41590-020-0762-x#data-availability May be hard to get data, deposited in genome sequence archive in China and listed as controlled access
A large scRNA-seq/VDJ COVID19 study: https://www.sciencedirect.com/science/article/pii/S0092867420314446?via%3Dihub
@raysinensis having a wrapper that creates a cellbrowser that includes VDJ data would definitely be useful. I know @kriemo has written some code to do this, but not sure if...
@kriemo this seems like a nice way to store additional vdj data in the object. Maybe we should just incorporate your version of the import function
Some existing tools for BCR/TCR analysis: https://immcantation.readthedocs.io/en/stable/
Some other tools for population diversity/similarity: https://www.rdocumentation.org/packages/divo/versions/1.0.1 https://github.com/kylebittinger/abdiv
A VDJ package that integrates with scanpy: https://icbi-lab.github.io/scirpy/index.html