pySCENIC
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aertslab
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 regula...
Hey! Another question - I tried to run SCENIC on the mouse ENCODE regions supplied at https://resources.aertslab.org/cistarget/ and got an error message (AssertionError). Based on what I've gleaned from other...
**Describe the bug** This may be a bug or a user-error, but I am unable to use custom thresholds in the binarize function **Steps to reproduce the behavior** 1. Command...
Crash when no signatures passed the filter: We ran into this issue with our NextFlow pipeline and a track database as a certain threshold was set to high, which caused...
Currently, running the cisTarget pruning step with incorrect/mismatched motif annotations and genome ranking databases (human vs mouse, for instance) produces an empty regulons file without any warning: ``` ,,Enrichment,Enrichment,Enrichment,Enrichment,Enrichment,Enrichment,Enrichment,Enrichment ,,AUC,NES,MotifSimilarityQvalue,OrthologousIdentity,Annotation,Context,TargetGenes,RankAtMax...
Hi pySCENIC developers, I tried with pySCENIC roughly, and the results were pretty good and interesting, which confirmed by our Seurat foundings. But I am not very sure how to...
Hi, @bramvds I have applied SCENIC to sc_matrix datasets using raw UMI counts, normalized UMI counts(logMat
@cflerin Hi, As #67 said,I also find the expression matrix generated by exportsForArboreto has no rowname (cell ids). The write.table format(row.names = FALSE) is wrong in exportsForArboreto function ,row.names should...
From the cli, the pyscenic ctx could only take one argument of `-o`, so one has to run twice to get the enriched motif and regulon, while each run is...
Hi, thanks for the great implementation! I'm trying to run `aucell` on 100k cells and 30k genes with some gene sets and always getting memory error (with `num_workers=1`).First, I need...
When trying load a custom motif file, the following error occurs: ``` motifEnr = prune2df(dbs, modules, MOTIF_ANNOTATIONS_FNAME, client_or_address=customClient) ValueError: Usecols do not match columns, columns expected but not found: ['orthologous_identity',...