search

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
220 stars 34 forks source link

Can Scirpy be used for the analysis of regular RNA-seq sequencing data? #417

Open yirenheihei opened 1 year ago

yirenheihei commented 1 year ago

Hello! This tool is excellent. Currently, I have a set of regular RNA-seq sequencing data, and I would like to know if it can be used to analyze such data. thank you

grst commented 1 year ago

Hi,

the short answer is: No, the scirpy receptor model is currently inherently limited to at most two pairs of receptors per cell.

The longer answer: As a workaround, you could represent each individual alpha or beta chain as an individual cell. But that way you will likely run into scalability issues very soon.

That said, the new data structure released with v0.13 could already represent bulk data and other receptor models. As we work on scalability issues, bulk analysis might become a supported option at some point in the future.

Rafael-Silva-Oliveira commented 2 weeks ago

@grst Any news on this? :) Would be super cool to expand this to bulk as well (or have a tutorial on this)

grst commented 2 weeks ago

Not really :(

We definitely plan to expand into spatial at some point (#354), depending on the protocols we support this will also require supporting bulk data. But I can't provide any timelines currently.