Code for the Brassica oleracea/rapa/napus genomic comparison.
Most of these folders are RStudio projects that can be opened in RStudio.
Code and RStudio project is under GO_Enrichment/
R-code for the stacked barplots for the R-genes can be found in R_Gene_Analysis/
R-code for pangenome size modeling is in the folder Modeling/
R-code for the Venn-diagram plots are in FinalPanPanVenn/
R-code for the variable genes vs core genes is in Visualise_Core_Variable_A_vs_C/
R-code for the PCA plots and animations are in Cluster_Napus_A_and_C_PAV/
These contain the XGBoost and Shapley values work.
You can launch them on binder:
Or navigate to the notebooks folder.