iPython, Revigo, mini eyes, DESeq, iPath, github, galaxy, SQLshare, WGNWCWGNCWGC… we’ve learned a lot of new words.
By this point, we’ve looked at the transcriptome and the differentially expressed genes in many different ways! This morning Casey and I finished off our attempts with iPath, so now we know how to use that. Check out the interesting figure in my notebook. I’ve also included notes on how to use it, though of course it has limitations. Maybe more of a viewing/ brainstorming tool?
It was also really interesting to learn a new R package from Lauren for analyzing genes that are expressed together!
I worked with the transcriptome itself in the afternoon. My goal is to graph the proportion of contains that match to GO slim terms in iPython for molecular functions, cellular processes, and biological processes for both the whole transcriptome and the ones that are annotated as echinoderms to see what we have. We’ll see if this fits into the overall plan down the line, but I thought it was an interesting way to delve further into the genes that are present. I’ve started that in my script at the process level and it actually is very similar to the division of processes for the whole transcriptome that we did on Tuesday –