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scverse / scirpy

A scanpy extension to analyse single-cell TCR and BCR data.
https://scirpy.scverse.org/en/latest/
BSD 3-Clause "New" or "Revised" License
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CDR3 convergence #23

Closed grst closed 3 years ago

grst commented 4 years ago

In GitLab by @szabogtamas on Feb 11, 2020, 16:00

I think we need to think again about how to compute the convergence and how useful it is in the context of single cell data. In our example dataset, it appears so occur at negligible rates and doesn't make sense to be visualized as a barplot. Finally, I believe it measures something similar as TCR-dist.

Ideas:

The CDR3 convergence is currently hidden from the public API, but the preliminary code is still in _plotting._cdr_convergence.

grst commented 4 years ago

In GitLab by @grst on Mar 16, 2020, 15:20

changed title from {-CDR3 convergence as a single measur-}e to {+Refactor CDR3 convergenc+}e

grst commented 4 years ago

In GitLab by @grst on Mar 16, 2020, 15:20

changed the description

grst commented 4 years ago

In GitLab by @grst on Mar 16, 2020, 15:28

In any case, it can be computed with tl.clip_and_count - no additional tool needed.

grst commented 4 years ago

In GitLab by @grst on Mar 20, 2020, 18:15

changed title from {-Refactor -}CDR3 convergence to CDR3 convergence

grst commented 4 years ago

In GitLab by @grst on Apr 6, 2020, 20:08

In any case, it can be computed with tl.clip_and_count - no additional tool needed.

not sure if this is actually true...

Anyway, to some extent this is now possible by comparing the clonotype definitions based on nucleotides and amino acids. Could still be wrapped in a nice tool.

I still need to think, though, if it's best to rely on the clonotype-definitions for that or do it independently of that.

grst commented 4 years ago

In GitLab by @szabogtamas on Apr 7, 2020, 09:36

Maybe we could offer a tool that accepts a pair of clonotype definitions (nt-based and aa-based by default) and returns the convergence from the first to the second. The user could then choose to use it as a measure of convergence of nts to aas or aas to alignment-based groups. I would not make it independent of the clonotype definition tool.

grst commented 4 years ago

In GitLab by @grst on Apr 7, 2020, 09:43

that's a great idea! way more flexible and also allows e.g. to compare alignment to identity