Brassica oleracea/rapa/napus code

Code for the Brassica oleracea/rapa/napus genomic comparison.

Most of these folders are RStudio projects that can be opened in RStudio.

GO enrichment

Code and RStudio project is under GO_Enrichment/

Resistance gene analysis

R-code for the stacked barplots for the R-genes can be found in R_Gene_Analysis/

Pangenome modeling

R-code for pangenome size modeling is in the folder Modeling/

Venn diagram plots

R-code for the Venn-diagram plots are in FinalPanPanVenn/

Core vs. variable genes plots

R-code for the variable genes vs core genes is in Visualise_Core_Variable_A_vs_C/

PCA plots

R-code for the PCA plots and animations are in Cluster_Napus_A_and_C_PAV/

Notebooks

These contain the XGBoost and Shapley values work.

You can launch them on binder:

Or navigate to the notebooks folder.