Chris C Flerin
Chris C Flerin
A recurring problem is that the GRN inference step of pySCENIC (using [Arboreto](https://github.com/tmoerman/arboreto)'s GRNBoost2/GENIE3 implementation) fails to complete successfully. This seems to be due to issues with newer Dask releases...
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...
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',...
Using the pySCENIC 0.9.4 CLI, I get the following error on the ctx step. This seems to be related to the most recent version of dask (v1.1.0), since when I...
Currently 10x multiome data (and some Cell Ranger versions) are not supported by `calculate_saturation_10x_samples.py`. There are different paths to the summary metrics file for multiome, RNA and ATAC, and these...
I'm running Arboreto's implementation of GRNBoost2 via the pySCENIC command line, but I figured this issue probably belongs here. I get the following warning, which repeats a number of times...