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saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
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Liana to compare conditions #80

Closed nasjr08 closed 1 year ago

nasjr08 commented 1 year ago

The liana resource is a terrific tool for assessment of cell-cell communication but I was wondering if an implementation of the resource that incorporates multi-condition datasets is available. in other words, If I have a dataset from disease and control where the same celltypes are captured, I would like to compare how cell-cell communication changes between disease and control. CellChat is an example of one of the resources that has introduced this functionality recently.

Is this something that is available anywhere or this something that is in the works? Further, if I was to split my seuratobj by the conditions and perform the analysis separately, can I deduce changes in L-R communication or would this methodology be invalid? Note that this is something that is performed in the CellChat Resource as shown here

Any advice would be much appreciated!

Thank you, Naseer

dbdimitrov commented 1 year ago

Hey Naseer,

Thanks for using LIANA. Indeed, I have implemented a solution for multi-condition (context) data sets in which we use a factorization approach (Tensor-cell2cell) to find hidden CCC patterns.

https://saezlab.github.io/liana/articles/liana_cc2tensor.html

We are also working on providing a protocols manuscript with more in-depth explanations. Will share it here once public.

nasjr08 commented 1 year ago

Thank you! I'll check it out and have a go!