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aertslab / SCENIC

SCENIC is an R package to infer 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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How to get the file tSNE_AUC_50pcs_50perpl.Rds and 3.4_regulonAUC.Rds #167

Open JingleW opened 3 years ago

JingleW commented 3 years ago

I run "runSCENIC_1_coexNetwork2modules(scenicOptions)" and runSCENIC_2_createRegulons(scenicOptions)" successfully without reporting an error. However, running SCENIC_3_scoreCells as "scenicOptions <- runSCENIC_3_scoreCells(scenicOptions, exprMat_filtered)" produced an error: Error in .AUCell_calcAUC(geneSets = geneSets, rankings = rankings, nCores = nCores, : Valid 'mctype': 'snow' or 'doMC'. Then, I followed https://github.com/aertslab/SCENIC/issues/152 to change the ncores =1, and it seemed working without reporting any error. However, when running "aucellApp <- plotTsne_AUCellApp(scenicOptions, exprMat_filtered)" or "regulonAUC <- loadInt(scenicOptions, "aucell_regulonAUC")", errors occurred becaused there were no files named “int/tSNE_AUC_50pcs_50perpl.Rds" and "int/3.4_regulonAUC.Rds". There is only 3.1_regulons_forAUCell.Rds in "int". Could anyone help to fix this problem? Which step produced the file starting with 3.x in the "int"? Thanks very much.

vickreiner commented 1 year ago

Hi! Maybe I am a bit late to the party, but I am having this issue too. Running AUCell 1.21.2 (Was not able to install 1.3, so I also followed the nCores = 1 fix as @JingleW. Are there any updates?

Thanks!