Thursday, December 27, 2018
Hey Galaxy People! Want easy proteo-transcriptomics!??!
Edit: Forgot paper link. Here!
Galaxy is one of the biggest players in the genomics/transcriptomics playground. As I understand it (from listening to smart friends in these fields):
1) Loads and loads of tools
2) You don't have to be a super coding expert
3) You don't get access to super cool new code until someone integrates it, but the community is big and active enough that the only people that get access to new tools faster -- are the super coding experts
Galaxy for proteomics (often referred to as GalaxyP) hasn't been as ubiquitous in our realm -- we've got our camps like TPP, MaxQuant, PD, CompOmics, OpenMS, etc.,.
GalaxyP shouldn't be ignored, though, it's an amazing tool for the (seemingly much more common) bioinformaticians coming from the genomics realm to jump right into ours.
QuanTP is a great new gap bridging tool! You can statistically correlate the transcript IDs with the proteomics data within this! What else can do this? Perseus -- I think, but you'd have to work all the data up into the right formats which would require loads of preprocessing from both sides. (I could be wrong here, of course.) In Galaxy you'd already have all the transcript processing tools available and the proteomics tools.
....Yes. I felt very stupid while making this. And while posting it. But it's done now!