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Partie applicative d'AgroMetInfo.

metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.

Source code of BIP software (Biological Image Processing)

FAIDARE: FAIR Data-finder for Agronomic Research

It provides web services (based on the BrAPI standard) and a web interface with easy to use filters to facilitates the access to plant datasets from a federation of sources.

part of the ANR D2KAB project, this repository is dedicated to the construction of semantic resources (RDF dataset and OWL ontologies) that will represent plant phenological development stages for agricultural practices.

DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.

This tool is expected to be easily customizable for specific filters, environments, or data schemas.

Edition 2026 de la journée SHINY::INRAE - 28 janvier 2026 https://sk8.pages-forge.inrae.fr/journee_shiny_inrae/edition_2026

This repository is a toolbox for PFEM's GitLab projects: templates for README, CI/CD, docker images, ...

A few notebooks for users and developers, showing how to use STAC to manipulate geospatial data.

RADIS - Retrieve Agronomic Data in a Sector, R package support : https://umr-g-eau.pages-forge.inrae.fr/radis

The radis package aims to facilitate the extraction of environmental data from various cartographic or spatial sources or APIs. It allows for the retrieval of this information using specific spatial shape. This package also formats the extracted data in a way that makes it easily exploitable for further analysis.

Docs : https://optirrighive.pages.mia.inra.fr/OptirrigCORE

What is “OptirrigCORE” package ? The OptirrigCORE package in R is based on the Optirrig model. It facilitates the extraction and formatting of observation data used by the model, as well as the integration of plant, soil and yield descriptions. It supports various analytical methods, such as Ex-Post and Ex-Ante analyses, with a view to drawing up an optimised irrigation schedule based on the criteria. The package includes all the calculation tools needed to describe biophysical processes with a generalist approach. It can be used as a dependency or complement to modify and reinterpret biophysical descriptions. What’s more, it automates the modeling process, the description of biophysical processes and the analysis of results and performance, guaranteeing a reproducible approach. It also makes it easy to compile results in automated reports.

This project is the source repository of the CRAN package 'hicream' https://cran.r-project.org/package=hicream.

It performs Hi-C data differential analysis based on pixel-level differential analysis and a post hoc inference strategy to quantify signal in clusters of pixels. Clusters of pixels are obtained through a connectivity-constrained two-dimensional hierarchical clustering.

A package build on top of airGRiwrm containing helper functions for pre-processing data and vignettes with a complete example of an integrated hydrological model setup from scratch and publicly available data.

SIDO (Système d’Information pour les Données Orphelines) est une application web qui permet de déposer les données récoltées par des sources de données orphelines, c'est-à-dire qui ne disposent pas de système d’information, dans une base de données dédiée. tickets

OpenFLUID framework and applications