I am working with TCGA data and I would like to divide cases into different groups with different activity levels of given transcription factors. Then I would like to perform for e.g. differrential expression analysis. Recently I learned about ISMARA web-tool which estimates TF activity using the expression levels of it's targer genes but it requires raw sequencing data which are not freely available in TCGA database. I think that it can be done using counts data but I do not know any tools for this. Can you tell me what can I use? Any R packages?
Ewentually, what can I use to find target genes of transcription factors?