It's mostly just a flowery extra word in there when you also have the word "target".
If you imagine a signalling pathway as a river/stream, then you have some parts of the pathway that are toward the beginning of the river, and you have some that are towards the end of the river, but up/downstream really all depends on where on the river your ...
pyrpipe claims to be a one-stop python library for RNA-seq analysis. Here is an illustration from their paper:
Furthermore, I would like to draw attention to ENCODE's official RNA-seq pipeline, which is actively maintained on ENCODE-DCC's GitHub repository.