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python

GenoFig is a tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It was designed to be as easy to use as possible for biologists.

This open access, modular, worflow for Hyperspectral Image data analyses enables : the opening and management of HSI files, a customized preprocessing of image data (deblurring and normalization steps), segmentation of objects, extract mean spectra of objects, then can perform machine learning analyses of data blocks (PLS, Random Forest are implemented). Additional feature include the generation of AI-predicted map of chemical compounds. Data can then be exported in various format.

xaaxaam is a set of scripts, written in R and python, aiming at producing high-resolution land-use maps from multi-sensors satellite imagery and ground-truth polygons.

Single-cell transcriptomic (SCT) analysis is essential for resolving cellular heterogeneity and uncovering the molecular foundations of development, physiology, and environmental responses. Despite its increasing importance, robust, reproducible, and broadly applicable SCT analytical tools remain largely restricted to well-annotated animal systems. This limitation poses significant challenges for biologists working on non-model species and poorly characterized tissues, where gene annotation is sparse and computational expertise is often limited.

We developed a stable, end-to-end SCT analysis pipeline designed to be accessible to biologists with little training in bioinformatics and applicable to species and tissues with limited genomic annotation. Built on the Seurat framework and complemented with additional tools, the pipeline supports any organism by automatically generating R-compatible annotation packages from basic genome files. It integrates standardized workflows for data preprocessing, quality control, clustering, biomarker identification, and gene set enrichment analysis within a fixed Snakemake framework, ensuring high reproducibility. By minimizing coding requirements, the pipeline enables rigorous, biologically informed SCT analyses across diverse experimental systems.

This repository contains the python code of the Marked-Release-Recapture simulator.

SATLAND is an application to detect and characterize hotspots of change. It is based on Python libraries (xarray, Bfast, rasterio for back-end, Streamlit for Front-End)

SETIER² (Capteurs et centrales d'acquisition low-tech pour les eaux résiduaires) est un projet de recherche open hardware Le projet SETIER² vise à démocratiser la surveillance de la quantité et qualité des eaux usées en développant des solutions de mesure accessibles, fiables et open source. SETIER² propose des alternatives DIY

Aide à la configuration et à l'alimentation en données d'un système d'information construit sur la norme OGC Sensorthings API.

Python package to download the tile table with urls of LIDAR-HD point cloud, DTM, DSM or DHM.

It contains the simulator of the model DISTIGRI describe in the work https://link.springer.com/article/10.1007/s10530-023-03062-y

Python bindings for the evalhyd utility

This repository contains a set of script for the acquisition and processing of thermal and visible images from FLIR A655sc and Daheng MER2 industrial camera as part of the LEAFPACE ERC project. All material in this repository is under the GNU GPL v3 and CC BY-SA licence. Please cite accordingly

Interekt (INTERactive Exploration of Kinematics and Tropisms) is a user-friendly software for tracking and modeling plant motions.

Ce dépôt donne à voir les résultats de l'expérimentation menée de façon transversale entre les pôles SENS, ASTRA, Num4Sci pour l'identification et la classification automatique des publications appartenant au domaine des Sciences et Recherches Participatives.

Cette expérimentation avait pour but de tester les bénéfices potentiels de l'utilisation de modèles de langues, LLM, pour l'automatisation de la catégorisation de publications scientifiques.

Contribution à la réalisation du "pilote" INRAE, dans le cadre du programme européen GraspOS

Gitlab Pages: https://egfv.pages-forge.inrae.fr/bioinfo/jbrowse-batch-submission

https://lindangulopez.streamlit.app/