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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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SCTransform normalised data or regular log normalised data for assessing gene-gene correlations with pySCENIC? #80

Open lucygarner opened 3 years ago

lucygarner commented 3 years ago

Hi,

I would like to use pySCENIC (https://www.nature.com/articles/s41596-020-0336-2) to identify modules of genes predicted to be regulated by a given transcription factor (regulons). I was wondering whether scRNA-seq data that has been normalised using SCTransform is suitable for this approach or whether this type of normalisation interferes with gene-gene correlation structures? The alternative options would be to use raw count data or count data normalised using the NormalizeData() function in Seurat.

Thanks for any insights that you can give.

Best wishes, Lucy