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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

mechanistic-statistical environement

https://olivier.bonnefon.pages.mia.inra.fr/mse/

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.

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...

The Orfeo ToolBox (OTB) extension for Deep Learning. Enable the use of TensorFlow models on Remote Sensing images. Provides OTB applications for patches sampling, model training, model inference, hybrid models, and so on.

Decloud is a framework to remove clouds in Sentinel-2 images from joint Sentinel-1 (SAR) and Sentinel-2 (Optical) images or time series.

This project is a custom version of CB-Geo MPM.

Run deep learning models from pytorch, tensorflow, keras, Caffe2, Microsoft Cognitive Toolkit, Apache MXNet, etc

Remote module for Orfeo ToolBox

massXpert2 (of the http://www.msxpertsuite.org software collection) is a desktop-oriented program that allows one to create polymer chemistry definitions. The definitions are then used to perform calculations in a desktop calculator-like manner and to perform sophisticated polymer sequence mass spectrometry simulations.

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

Code storage Area of the RECORD Project packages.

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

set of usefull mass spectrometry and proteomics utilities used by the PAPPSO team (http://pappso.inra.fr/). Get ion tables from peptides, SVG drawings of MS/MS annotated spectrum, expected intensity ratio of isotopes from a peptide....

C++ implementation of SpecOMS and new developments