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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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TF target genes in decoupleR analysis of scRNA-seq data #122

Closed JinSooJoo closed 5 months ago

JinSooJoo commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

Hi @JinSooJoo,

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