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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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Understanding scenicPlus settings and Outputs #469

Closed orian116 closed 1 month ago

orian116 commented 2 months ago

Hello. Thanks so much for the package! I had some basic questions about the package:

  1. Could you explain how scenicplus creates the pseudomultiome dataset? I recognize it's not a 1:1 relationship between the key_to_group_by set in the config.yaml file and the resulting AUC matrix has much less cells than either ATAC or RNA-seq matrices. Also on that, how did you decide the default nr_cells_per_metacells to be 10 and how does increasing or decreasing that number affect the results?
  2. I had some general questions about what the "Regions" in the eRegulon represent and how they are related to the TF and gene in terms of location on the genome. Does Scenicplus weigh differently TFs that regulate genes/regions on different chromosomes i.e TFS that are trans acting elements? Are these trans acting elements lower confidence than cis acting TFs i.e TFs that regulate the genes/regions on the same chromosome?