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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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[BUG]what is signatures_fname required by aucell? #467

Open caodudu opened 1 year ago

caodudu commented 1 year ago

when I try the code like this:

${pyscenic_path}/pyscenic aucell \
    ${inputs_loom} \
    ${output_path}/data.filt.reg.csv \
    --output ${output_path}/${project}_data.filt.out_SCENIC.loom \
    --num_workers 20

I find a file called 'signatures_fname' is required. So what is it? why others try to analyse don't need the file. usage: pyscenic aucell [-h] [-o OUTPUT] [-t] [-w] [--num_workers NUM_WORKERS] [--seed SEED] [--rank_threshold RANK_THRESHOLD] [--auc_threshold AUC_THRESHOLD] [--nes_threshold NES_THRESHOLD] [--cell_id_attribute CELL_ID_ATTRIBUTE] [--gene_attribute GENE_ATTRIBUTE] [--sparse] expression_mtx_fname signatures_fname pyscenic aucell: error: the following arguments are required: signatures_fname

VittoriaDBocchi commented 5 months ago

Hi! I have the same problem and error message. Where you able to solve it? Thanks!

caodudu commented 5 months ago

Hi! I have the same problem and error message. Where you able to solve it? Thanks!

Sorry, I did fix it but unfortunately I didn't record the solution. The advise is to utilize your script to test a demo dataset which has worked in others' computer.

wz0527 commented 4 months ago

Hi,

In the step of ctx, you can try to save the output file as gmt file, but not csv file. I resolved my error in this way. Hope it could help.