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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.