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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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Can Liana work on csv files #125

Closed Samir1703 closed 1 year ago

Samir1703 commented 1 year ago

Hey, I'm very new (literally started yesterday) to all this and I have almost no idea what I'm doing. I want to run ligand receptor analysis on a single cell dataset I have. I basically only have a csv file containing the genes and their relative expression per cluster. Can I run a Liana analysis on that csv or does it need to be a seurat object ?

dbdimitrov commented 1 year ago

Hi @Samir1703,

LIANA requires a Seurat or SingleCellExperiment object as input. So, you would need to convert the csv to those.

Samir1703 commented 1 year ago

Hello @dbdimitrov ! Thank you for your reply :) As I said I'm very new to all this. Would creating a seurat object out of a csv file containing gene expression per cluster work ? Something that goes like that Gene, Cluster 1, Cluster 2, Cluster 3 GeneA, ValueA1, Value A2 ...etc

Basically I annotated my single cell using cloupe and extracted the raw data for my manual annotation but in that I lose the data for individual cells and only have cluster gene expression

Any insight would help

Thanks

dbdimitrov commented 1 year ago

Hi @Samir1703,

Liana requires the information about individual cells to work, specifically it requires a count table with normalised counts and a corresponding cluster label for each cell.

Hope this helps.