I have an RNA-seq counts and phenotype dataset. I have used DESeq2 to identify the differentially expressed genes, and I have also conducted Gene Ontology and Gene Set Enrichment Analysis to get the biological function and enriched pathways.

I would now like to perform transcription factor enrichment analysis. But, I am not able to find a solid lead for how I can do this.

The RNA-seq dataset I have is for cancer cells with certain knockdowns.

I would be grateful if someone could guide me in the direction of how I can perform TFEA from the data I have.

I apologise if my question is very general.