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ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
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Missing CellSign_active_interactions and CellSign_active_interactions_deconvoluted files when running Method2 #156

Closed wfaalajr closed 7 months ago

wfaalajr commented 7 months ago

Hi! I am currently using CellphoneDB v5 and database v5. I noticed that the final output dictionary cpdb_results contains all the output as mentioned in the tutorial:

list(cpdb_results.keys())

Gives:

['deconvoluted', 'deconvoluted_percents', 'means', 'pvalues', 'significant_means', 'CellSign_active_interactions', 'CellSign_active_interactions_deconvoluted', 'interaction_scores']

But when I check my output directory, the files for CellSign_active_interactions and CellSign_active_interactions_deconvoluted are not there. Has this happened to anyone?

datasome commented 7 months ago

Hi wfaalajr,

Thanks you for using CellphoneDB and for your inquiry. Did you provide active_tfs_filepath argument in your statistical analysis call? (Please see https://cellphonedb.readthedocs.io/en/latest/RESULTS-DOCUMENTATION.html#tf-activity-status-cellsign-module for more information). If not, the CellSign* files are not saved (as CellSign module returns empty matrices as a result). Hope that helps.

Best,

Robert.

wfaalajr commented 5 months ago

@winglet0996 yeah XD i guess it’s important for some applications (e.g. to verify transcriptional activation of downstream genes) in which case supplying the TFs file is necessary..but the format of the file is too bothersome to make (i’m just lazy i guess). just do the qPCR and be done with it.