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rbloom5 / ImmuneRep

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Feature analysis on MS patients #6

Open rbloom5 opened 9 years ago

rbloom5 commented 9 years ago

Clustering, frequency statistics etc. on simple features like V segment usage, J segment usage, CDR length, composition etc etc. The goal would be to try and find simple features that distinguish MS from healthy patients.

rbloom5 commented 9 years ago

For example - others have shown that VH4 is used more often in MS patients than in controls. It would be interesting to see if that is true in our data, and find other things like that.

rzeller commented 9 years ago

I have some basic V, D, and J segment usage analysis up and running (currently on the feature-analysis branch). My next step will be to tackle CDR length and composition stuff. I need to find some good examples in the literature. I'm definitely open to any suggestions for where to take this.

rbloom5 commented 9 years ago

Yea, we are definitely venturing into uncharted territory a bit here. I think the following references are pretty good - but we can definitely talk more about it this afternoon

http://www.ncbi.nlm.nih.gov/pubmed/23390249 http://www.ncbi.nlm.nih.gov/pubmed/25100740 http://www.ncbi.nlm.nih.gov/pubmed/23160197

as well as a lot of this stuff: http://www.hackbio.com/cv/