I show you how to do and plot GSEA using predefined gene ontology gene sets as well as custom user input genes in python. This easily integrates into other differential expression or single-cell analysis pipelines in python and only requires a few lines of code.
Note: It is better practice to not filter out the non-DE genes. In this case, you will also need to lower the default permutation_num in the gp.prerank function to something like: permutation_num = 100
Notebook:
github.com/mou...
Негізгі бет Simple guide to GSEA and plotting in python
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