I give MaxQuant and Perseus a tough time, and will probably continue to for the duration, despite the fact that -- if you can get them running and keep them running -- and are patient (for MaxQuant, I've never waited for Perseus to do anything, fast!) the data they produce is totally legit. How it gets there? Fuzzy on that, but this summer I added to my pile of Perseus installations that are labeled by what features work and don't work the ultimate prize -- uMAP, tSNE, and WGCNA
If you do want to know what the first two are, this guy walks you through them slowly using some simple geometric models and other tools so well that you'll piece together the clues from different clips of Youtube videos from MaxQuant summer schools over the last 4 years to get a version of your Perseus functional so you can use it. You install plugins and R packages and make everything work together. WGCNA is powerful enought to draw conclusions from data as lousy as microarrays, so imagine what it can do to your well-controlled proteomics data!
What was I typing....oh yeah! MetaNetwork!
What if you could have clustering and enrichment power from people who make really straight-forward and powerful graphic user interfaces?
I gotta go and Docker is reminding me that the way they do free vs. nonfree changed in 2022 and I don't want to read all the things it says, so I can't run stuff through this one myself, but you can get MetaNetwork on Github here!
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