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MineXpert2 (of the http://www.msxpertsuite.org software collection) is a desktop-oriented program that allows one to visualize mass spectrometric data in their full MS^n depth. Sophisticated mouse-driven mass data integrations are easily performed. It is the continuation of mineXpert2, ported to the rewrittent libXpertMass and libXpertMassGui libraries.

PAPPSOms++ is a comprehensive C++ library including useful functions to handle mass spectrometric data, either in a proteomics setting or for data visualization. Abstractions include peptides, proteins, isotopic clusters, mass/drift spectra...

mechanistic-statistical environment

https://msegrp.pages-forge.inrae.fr/mse

Model to simulate the spread of Map within and between herds via trade movements between dairy herds. Some control measures can be applied. Model is mechanistic and data-driven, stochastic, discrete-time and individual-based.

GroupingProtein does filtering, protein inference and grouping of mass MS/MS identification result (thousands of samples, high resolution mass spectrometers)

i2MassChroQ (identification & inference -- mass chromatogram quantification) is the successor of X!TandemPipeline-Java. Following a full rewrite in C++17 and integration of the MassChroQ module, i2MassChroQ features a quantitative proteomics solution

A bi-objective optimization solver for graphical models.