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GenMAPP is an application designed to visualize genomic data on maps representing biological pathways and other groupings of genes. GenMAPP also includes tools for performing global analysis of genomic data in the context of the Gene Ontology hierarchy.
MSQuant is a tool for quantitative proteomics/mass spectrometry and processes
spectra and LC runs to find
quantitative information about proteins and peptides. Though
automated it also allows manual inspection and change.