TF target genes in decoupleR analysis of scRNA-seq data

[JinSooJoo]

Hello, first of all I appreciate the fantastic package.
The decoupleR provides target genes of defined TF in bulk-seq data analysis.
I'm wondering if I can verify the target genes of specific TF analysed by decoupleR in scRNA-seq data in R.

Thanks!
Jin Soo Joo

[PauBadiaM]

Hi @JinSooJoo,

Sorry I do not fully understand what you mean here by "verify", but if your question is can decoupleR be run on single-cell resolution data the answer is yes. You can check one of the many vignettes in R or python.

[JinSooJoo]

Hi @PauBadiaM , thanks for your help.
Sorry for confusing, I ran decoupleR on seurat object and got heatmap plot of differential activities of TFs.
And I want to know which genes are at downstream each TFs shown in heatmap plot.
I checked vignettes in R that bulk-seq analysis can show DEGs of each TFs, so can I know the downstream genes of each TFs as in scRNA-seq data also?
Thanks a lot!

[PauBadiaM]

Hi @JinSooJoo,

You could perform pseudobulk analysis as shown in this vignette (only in Python sorry). Hope this is helpful!