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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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prune2df empty #493

Open GeneVector5 opened 1 year ago

GeneVector5 commented 1 year ago

I am working on human related sCRNA data.

human_ranking_dbs_FILENAMEs_abrev = "hg38__*.mc9nr.genes_vs_motifs.rankings.feather" human_motif_annotations_FILENAME = 'motifs-v9-nr.hgnc-m0.001-o0.0.tbl'

I am getting an empty dataframe after calling prune2df but I do not know what this means. There are 150 modules 

modules = list(modules_from_adjacencies(adjacencies_df, expression_matrix_df))

with ProgressBar():
    df = prune2df(dbs, modules, MOTIF_ANNOTATIONS_FILENAME)

The dataframe comes out empty, what does this mean?