Projects with this topic
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Progressive examples and tests showing how to pass multiple R data types through Rcpp to Fortran and return results back to R.
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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.
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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.
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FreezeR is a R package which implements a Bayesian model aiming at deciphering main drivers of tree buds freezing.
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The 'rsiwaa' R package provides an API to help using, in R language, a Siwaa tool or a Siwaa workflow. It allows to upload input files, run the tool or the workflow, survey the running progression, and finally download output files.
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This repository contains the scripts used to produce the experiments presented in
Jorge E., Hocking T.D., Neuvial P., Vialaneix N., and Foissac S. (2025) Posthoc inference for interpretable Hi-C differential analysis. preprint
These experiments aims at illustrating the use of the R package hicream that performs differential analysis of Hi-C data.
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F3MR is a R package that help to analyze food microbiome omics data based on dedicated and curated metabolic modules based on extensive literature review. It belongs to F3M software suite developed by INRAE Food Microbial Ecology lab
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Replication repository for the article "A comprehensive review and benchmark of differential analysis tools for Hi-C data"
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Cette application permet l'exploration, l'interrogation, la visualisation et l’interprétation fonctionnelle d'un ensemble pre-processé de données épigénétiques (ATAC-seq) correspondant à la régulation temporelle des réseaux de transcription pendant la régénération des axones du système nerveux central chez le poisson zèbre.
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Cette application permet aux utilisateurs de visualiser les caractéristiques physicochimiques de plus de 100 produits, ainsi que de comparer entre eux différents produits avec des boxplots.
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R script to compute trees cartesian coordinates from field measures in polar coordinates.
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Learn how to build a shiny application
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Développement d’une petite application Shiny et déploiement de celle-ci avec sk8, animé par Amandine Velt (SVQV) et Joseph Tran (EGFV) [AG CATI BARIC La Rochelle, 26-28/03/2024]
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Learn how to build a shiny application
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Développement d’une petite application Shiny et déploiement de celle-ci avec sk8, animé par Amandine Velt (SVQV) et Joseph Tran (EGFV) [AG CATI BARIC La Rochelle, 26-28/03/2024]
slides: https://joseph.tran.pages.mia.inra.fr/quarto-shiny-sk8
tutoriel: https://forgemia.inra.fr/joseph.tran/shiny-tutorial
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R script to manipulate peptide quantification data
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