"Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China" by Michelle Baker, Xibin Zhang, Alexandre Maciel-Guerra, Kubra Babaarslan, Yinping Dong, Wei Wang, Yujie Hu, David Renney, Longhai Liu, Hui Li, Muhammad Hossain, Stephan Heeb, Zhiqin Tong, Nicole Pearcy, Meimei Zhang, Yingzhi Geng, Li Zhao, Zhihui Hao, Nicola Senin, Junshi Chen, Zixin Peng, Fengqin Li, and Tania Dottorini
Any questions should be made to the corresponding author Dr Tania Dottorini (Tania.Dottorini@nottingham.ac.uk)
Nine scripts are available:
- Population Structure Analysis: calculate_GSC.py and weighted_chi_square.py
- SNP network (Figure S14): snp_network.py
- The classification framework (Figures S8 and S9): Ecoli_ML_pipeline.py and Salmonella_ML_pipeline.py
- The ML features network (Figure S12): network_ML_features.py
- The known AMR genes network (Figure 6): network_AMR_genes.py
- Shap Analysis (Figures 4 and 5): shap_Ecoli.py and shap_Salmonella.py