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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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SCENIC+ prepare_menr error: TypeError unbound method set.union() needs an argument #442

Closed jklvrt closed 3 months ago

jklvrt commented 3 months ago

Hi,

Managed to reach the SCENIC+ steps, but while running through CLI reached this error at the prepare_menr step (images attached of log file and CL output). Any ideas/help would be greatly appreciated

Screenshot 2024-08-04 at 13 28 54 Screenshot 2024-08-04 at 13 28 21
jklvrt commented 3 months ago

was a mistake in input setup.... :)

irepansalvador commented 3 months ago

Hi @jklvrt could you please elaborate on the input setup mistake you found? I am getting exactly the same prepare_menr error but I haven't yet figure out what could be happening. Any help would be appreciated. Irepan

jklvrt commented 3 months ago

My input file setup was wrong, specifically the 'path_to_motif_annotations' variable was wrongly set to just the tf list file, instead of the actual motif annotation table : motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl, Hope this is the reason behind your error

irepansalvador commented 3 months ago

Thanks for your prompt response, this doesnt seem to be the reason behind my error as in my case my input file is pointing at the motif annotation table. I suppose my error is related to the fact I am using scenicplus with a different species from the default (I am using pig as species), as I managed to run scenicplus successfully with mouse. I will create a new issue describing my error. thanks again!

Yiming-Huang-neuron commented 2 months ago

Hi, I met the same mistake. I fail run on mouse data, but succeed on human data. I used the matching tf list file which I have checked as input. @irepansalvador did you fix your mistakes?

irepansalvador commented 2 months ago

Hi @Yiming-Huang-neuron , I managed to run the whole pipeline. In my case I needed to create a custom genome_annotation file and also a path_to_motif_annotations file, as I was dealing with another species. I didn't have this error when analysing mouse data though.

Yiming-Huang-neuron commented 1 month ago

@irepansalvador Hi, thanks for your reply, but I still have not fixed this mistake even after a week has passed. I wonder if it has to do with the threshold I set.

Best

Yiming