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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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Omnipath extension #147

Closed lindsdudley closed 2 months ago

lindsdudley commented 5 months ago

Hi liana group,

Thank you so much creating this amazing resource. I am trying to extend this to using omnipath to look at specific pathways. I am able to get the omnipath data but I am a little confused about the liana inputs it requires.testdata <- readRDS(file.path(liana_path , "testdata", "input", "testdata.rds"))

I have an RDS from saving the end of my liana resources but I am confused what the "test_data" and "input" are supposed to be.

Could you please advise?

dbdimitrov commented 5 months ago

Hi @lindsdudley,

Can you please share which tutorial is this from? Input data is usually a SingleCellExperiment or Seurat object. Does this help?