Num of genes after VST - Githubissues

satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

GNU General Public License v3.0

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Num of genes after VST #48

Closed haoyangz closed 4 years ago

haoyangz commented 4 years ago

I wish to get the residual for all the input gene, but I observed that the number of genes after VST is reduced. Could you please help me understand which step of the pipeline does this selection of gene corresponds to?

haoyangz commented 4 years ago

I found it is because with parameter min_cell =5, vst only keep genes that appear in >=5 cells.