SCENIC
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aertslab
0 genes available in RcisTarget database
Dear developer, When I generated the geneFiltering function, I found that 0 genes available in RcisTarget database. The object "exprMat" is from Seurat object. And the above code is the same as your tutorial.
Maximum value in the expression matrix: 10 Ratio of detected vs non-detected: Inf Number of counts (in the dataset units) per gene: Min. 1st Qu. Median Mean 3rd Qu. Max. -1035.10 -121.23 -32.17 -12.17 70.13 1356.90 Number of cells in which each gene is detected: Min. 1st Qu. Median Mean 3rd Qu. Max. 147.0 655.0 714.0 682.2 763.0 1309.0
Number of genes left after applying the following filters (sequential): 11213 genes with counts per gene > 90 11213 genes detected in more than 30 cells 0 genes available in RcisTarget database
no genes available in RcisTarget database and I can't continue to run the SCENIC. Please help me find the problems. Thank you very much!
Dear Developer, I have same problem. could you help me to solve it? genesKept <- geneFiltering(exprMat, scenicOptions=scenicOptions, minCountsPerGene=3*.01ncol(exprMat), minSamples=ncol(exprMat).01) Maximum value in the expression matrix: 56505 Ratio of detected vs non-detected: 0.11 Number of counts (in the dataset units) per gene: Min. 1st Qu. Median Mean 3rd Qu. Max. 0 61 1276 42116 10761 101433110 Number of cells in which each gene is detected: Min. 1st Qu. Median Mean 3rd Qu. Max. 0 58 1108 6627 8445 68934
Number of genes left after applying the following filters (sequential): 11927 genes with counts per gene > 2089.35 11907 genes detected in more than 696.45 cells Using the column 'features' as feature index for the ranking database. 0 genes available in RcisTarget database
Hi， I have the same problem when using mouse single cell database, only 18 genes available in RcisTarget database. Can you have the methods to solve it? Thanks!
