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Pipeline to run CMS in large-scale analyses

Data and code of the article Brault et al., Effect of nirsevimab on hospitalisations for respiratory syncytial virus bronchiolitis in France, 2023–24: a modelling study, The Lancet Child & Adolescent Health, 2024.

Course material for the part about R and RStudio of the PhD course.

A python package to impute the SNP summary statistics from neighboring SNPs summary statistics by taking advantage of linkage desiquilibrium

Collection of R scripts and pipelines for the PvSTATEM project.

Git repository to host The PvSeroTAT RShiny app. This app provides a user-friendly interface to apply classification algorithms to detect recent infections by Plasmodium vivax, as detailed in the recent paper by Longley et al. (https://doi.org/10.1038/s41591-020-0841-4)

Individual-based model of P. vivax transmission

Data and code of the article Rasoamalala et al. "Unraveling the role of rat and flea population dynamics on the seasonality of plague epidemics in Madagascar", Proceedings of the National Academy of Sciences (2025).

Sources for the server running at http://hub05.hosting.pasteur.fr/NMD_complexes/ Allows exploration of interactions around NMD complexes (Dehecq et al., EMBOJ 2018)

Code repository for the paper "An algorithm to build synthetic temporal contact networks based on close-proximity interactions data"

Repository containing scripts and data for the paper "Hozé et al., Lancet Public Health, Monitoring the proportion of the population infected by SARS-CoV-2 using age-stratified hospitalisation and serological data: a modelling study"

MeRIP-Seq pipeline analysis for m6a methylation site detection Author: Christophe Bécavin, Hub Bioinformatic and Biostatistic, Institut Pasteur