Karaniare/PfWGS-DRscanner: Genome-wide Scans for Locus Association with Antimalarial Drug Responses in Plasmodium falciparum

This repository provides scripts to perform genome-wide scans for signatures of selection and recombination in Plasmodium falciparum using population genomic data. It also includes scripts for mixed effets-based genotype-phenotype association analysis, the temporal trend analysis of haplotype prevalence and haplotype frequency plotting. The workflows implemented here were developed in the context of the PX1 manuscript, but they are generalizable and can be applied to other datasets with minimal adaptation.