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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.

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

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...

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

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.

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.

Meteor (Metagenomic Explorator), a software for profiling metagenomic data at gene level

erecord web services, web solutions for VLE models of RECORD platform

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