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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...

Construction and Analysis of Protein-Protein Interactions (PPI) NETWORKS for complexes and biological processes

Lightweight C++ and Java library to produce Open Document Spreadsheet (.ods) files. The main goal is to write data as simply as writing it to a simple text file (csv or tsv). Libodsstream allows yout to read and write ODS files as stream

MassChroQ (Mass Chromatogram Quantification) is a powerful and versatile software that performs retention time alignment, XIC extraction, peak detection and quantification on data obtained from liquid chromatography-mass spectrometry techniques.

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

mechanistic-statistical environement

The aim of this project is to provide an R package for big integer (and big rational) computations. This is achieved via an C++ interface to the GNU MP ("GMP") library, and S3 classes "bigz", "bigq", etc.

A library that contains a subset of the ProteoWizard libpwiz library with code mainly aimed at loading MS files (XML-based and MGF).

GSpace is a simulator for large genomic data, based on a generation-by-generation coalescent that takes into account small population size, recombination, and isolation by distance.

The SeSAM R package allows fully automatic construction of two successive genetic maps: a first one including an optimized subset of markers ensuring the robustness of orders to a given statistical threshold, and a second one including almost all polymorphic markers. It can handle all common types of biparental mapping populations, including progenies obtained from crossing heterozygous parents. In addition to the automatic procedure, SeSAM includes many functions for interactive mapping, file formats conversions, and generates many graphs useful to assess the quality of data and maps.

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

A library of Cost Function Networks and other graphical model instances (MRF, PWMaxSat,...).