P. falciparum population genetic in MALI
This repository holds all data and plotting scripts needed to reproduce plots from the paper "Genome-wide SNP analysis of Plasmodium falciparum show differentiation at drug resistance associated loci between malaria transmission settings in Southern Mali", by A. Coulibaly, M.F. Diop and A. Amambua-Ngwa et. al. This includes plots in the main text and in the supplemental material. In cases where the plotting data and scripts are located elsewhere, the relevant links are contained within the figure folder.
Dependencies
The following need to be installed and in the path...
- R (v4.0.3 (2020-10-10))
- adegenet
- ggplot2
- cowplot (v1.1.1)
- dplyr (v1.0.9)
- fdrtool
- finepop
- mmod
- moimix
- PopGenome (v2.7.5)
- patchwork (v1.1.1)
- pophelper (v2.3.1)
- rehh (v3.2.2)
- SNPRelate (v1.30.0)
- tess3r (v0.5.0)
- tidyverse (v1.3.2)
- LDheatmap
- Rstudio
- ADMIXTURE (v1.3.0)
- vcflib (v1.0.3)
- plink (v2.0)
- bcftools (v1.9)
- vcftools (v0.1.17)