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Collection of R scripts and pipelines for the PvSTATEM project.

Source of the shiny server that presents results obtained by large scale double mutant yeast screens (GIM): http://hub05.hosting.pasteur.fr/GIM_interactions/

sPYce is a since cell and single nucleus ATAC-seq integration method across different species implemented in Python.

pipeline nextflow

coGSEA with the SetRank Method

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

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).