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aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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[Tutorial] [246] export_gene_activity_to_loom important in SCENIC+ analyses? #177

Open yojetsharma opened 1 month ago

yojetsharma commented 1 month ago
  1. When I run export_gene_activity_to_loom , I get a "TypeError: '<' not supported between instances of 'float' and 'str'". Maybe because there some NaNs in my cell type_annotations? But export_region_accessibility_to_loom works smoothly.
  2. I checked the Cortex_pycisTopic tutorial but that ends with export_region_accessibility_to_loom. So, is this export_gene_activity_to_loom really necessary in SCENIC+ analyses? if yes, then how can I solve the aforementioned typeerror?
SeppeDeWinter commented 1 week ago

Hi @yojetsharma

For your first question: Could you share the entire stack trace including the exact command you ran?

For the second question: No, this function is not needed for the SCENIC+ analysis. So if you wish, you can skip it without issue.

All the best,

Seppe