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arnaud00013's Projects

fiji_mobile_gene_specific_popgen_scripts

This pipeline allows to call mobile genes SNVs and compute popGen metrics of interest from mobile gene alignment with samples metagenomic reads.

sars-cov-2-hpda-evolutionary-analysis

This repository contains a script for analyzing SARS-CoV-2 evolution in epitopes during the first two waves of the COVID-19 pandemic. The immunological data come from a high protein density array analysis of SARS-CoV-2 epitopes in 15 patients (N'Guessan A. et al., 2022). This script and the related data can be updated manually to integrate data from other waves or other sets of epitopes.

sars_cov_2_haplotypes_tajima_d_2020_time_series

Scripts and data used for analyzing the spread of SARS-CoV-2 haplotypes worldwide during the first and second waves (2020)

sc-eqtl

This repository contains the script to parse single-cell RNA-sequencing data and perform downstream analyses like variance partitioning and eQTL mapping

sodapop

Forward-time simulator for large-scale population dynamics and molecular evolution including pangenome evolution

wastewater_surveillance_pipeline

This repository contains a suite of tools for analyzing within-sample genetic diversity of SARS-CoV-2 in Wastewater (WW) samples

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