TypeError export_pseudobulk

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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TypeError export_pseudobulk #298

Closed skoturan closed 4 months ago

skoturan commented 4 months ago

TypeError export_pseudobulk

I'm trying to run the pycistopic tutorial for 10x multiome data. I come across the following error when I try to run "export_pseudobulk" :

TypeError: export_pseudobulk() got an unexpected keyword argument 'remove_duplicates'

Screenshots

Version

Python: 3.8
SCENIC+: 1.0.1.dev6+ge5ba6fc.d20240130

Could you please help? Thanks!

laki-spk commented 4 months ago

I am also getting the same error and same version. Could you please help? Thank you

SeppeDeWinter commented 4 months ago

Hi @laki-spk and @skoturan

This parameter has been removed as off this PR https://github.com/aertslab/pycisTopic/pull/105. This part of the code has been optimised and it now always removes duplicates.

You can just run the same code without this parameter.

All the best,

Seppe

skoturan commented 4 months ago

Thanks, it worked!