[small updates] Raw proteomics processing

broadinstitute / PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

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[small updates] Raw proteomics processing #39

Closed Munchic closed 1 year ago

Munchic commented 1 year ago

DIA-NN parameters make them the same as in the GUI by default
DIA-NN remove unused params in library generation and in search
Upgrade FragPipe to 19.1 and dependencies
Added developer documentation