Using decoupler to implement Cytosig analysis

[SNOL2]

Hi, thanks for this wonderful tool!
I was wondering if there is a tutorial for using decoupler to implement Cytosig analysis.
Thanks again!

[deeenes]

Hi,

You can follow the exact same procedure as for pathway activity inference. Instead of PROGENy, simply use CytoSig:

import decoupler as dc

cytosig = dc.get_resource('CytoSig')

dc.run_mlm(
    mat = adata,  # <- your single cell data
    net = cytosig,
    verbose = True,
)

adata.obsm['mlm_estimate']  # <- the results

[SNOL2]

Hi,

You can follow the exact same procedure as for pathway activity inference. Instead of PROGENy, simply use CytoSig:

import decoupler as dc

cytosig = dc.get_resource('CytoSig')

dc.run_mlm(
    mat = adata,  # <- your single cell data
    net = cytosig,
    verbose = True,
)

adata.obsm['mlm_estimate']  # <- the results

Got it! Thanks!