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ASSIGNEZ VOS MERGE REQUESTS à votre correspondant d'équipe/axe : @samuel.buchet (OpTeam), @leo.saulieres (DecA), @bcharlier (ASAP), @benjamin.linard (BioComp), @philippe.bordron (Genotoul) ou @rtrepos (RECORD)

Visualisation de données métagénomiques.

Projet de la version V2 de l'application des ORE.

Le projet est constitué de 2 sous projet :

La partie serveur qui fournit les web services de l'application

La partie UI qui fournit une interface VueJS permettant d'interroger ces Web Service

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.

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...

Présentation en ligne sur GitLab Pages

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.

https://genotoul-bioinfo.pages-forge.inrae.fr/d-genies/dgenies-new-proto-ui

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.

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.

Perform 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.

the ontology to describe the interaction between organisms and cultivated plants

R package to run MuSICA