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Hi,
Thanks for providing this wonderful tools. I am just wondering what format of the inputted gene expression would be better, raw count, or normalised one, such as log2(count+1), log2(TPM+1).
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I get the error when I run: scenicOptions
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Hi!
i was wondering, if i include two different ranking databases during the pySCENIC ctx step, which have either 10kb UP and down of TSS or 500bp up and 100 down annotations, then does pySCENIC in…
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Hi @tropfenameimer,
Thanks for the great tool!
I wanted to use pySCENIC tool in plant. So I create my own plant cisTarget databases with the tool "create_cisTarget_databases". Everything is ok …
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Got this error when trying to use run_mean with phospho data for kinase activity estimation:
Can't convert to .
Here is the tracback. If you need I can provide the input object as well.
Can'…
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# creating a dictionary of regulons:
regulons = {}
for i,r in pd.DataFrame(lf.ra.Regulons,index=lf.ra.Gene).iteritems():
regulons[i] = list(r[r==1].index.values)
Could you please specify ho…
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In part "04_TranscriptionFactor_activity_with_Dorothea", how are the TF activities calculated?
Or, what does it mean if a TF has a high or low NES? Wouldn't it mean that the associated genes are most…
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Hello Pau,
Thanks for implementing this. Installation works, but execution of main tutorial script fails. I think the pkl files were not distributed or downloaded in the main tutorial. Could you pl…
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**Describe the bug**
A clear and concise description of what the bug is.
When given a path for the loom files to be published (defined in .config file), an error occurs at the SCENIC:MERGE_MOTIF_T…
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Hello,
I have a question regarding AUCell scores of negative regulons.
I understand that the higher the expression of the factor targets in the cell, the higher the score.
So for negative regulons,…