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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.
Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.
Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data.
A pipeline for quantitative proteomics based upon isobaric tags
IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by...
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Structlab is a machine learning C++ framework for structured domains, which provides a toolbox of learning methods and tools for preprocessing and visualization. It also provides a GUI to setup elaborate experiments in a visual and intuitive way.