MouhamadSy/DrugResistance-Senegal-2013-2022

Code and analysis scripts for the study "Temporal and Spatial Dynamics of Antimalarial Drug Resistance in Senegal (2013-2022)" including SNPs plotting and Haplotype visualization, Regression model. # Temporal-and-Spatial-Dynamics-of-Antimalarial-Drug-Resistance-in-Senegal-2013-2022- Code and analysis scripts for the study "Temporal and Spatial Dynamics of Antimalarial Drug Resistance in Senegal (2013-2022)" including SNPs plotting and Haplotype visualization, Regression model. ## Description This repository contains Python and R scripts used in the study *"Temporal and Spatial Dynamics of Antimalarial Drug Resistance in Senegal (2013-2022)"*. The code includes data processing, SNP analysis, regression modeling, and figure generation, including Bayesian regression models. ## Tools and Pipelines Used - **Library preparation:** MaRS protocol - **Sequence data analysis:** Nf-NeST pipeline ## Repository Contents - `python/`: - `snp_analysis.py`: Scripts for processing SNP CSV files and generating plots. - `R/`: - `regression_models.R`: Scripts for regression analyses and Bayesian modeling using `rjags`. - `figures/`: Folder to store generated figures. - `data/`: Placeholder for input CSV files (not included for privacy/NCBI submission reasons). ## Dependencies ### Python - pandas - numpy - matplotlib - seaborn Install dependencies via pip: ```bash pip install pandas numpy matplotlib seaborn