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FAQ
Q1: ssGSEA missing p value and FDR?
A: The original ssGSEA alogrithm will not give you pval or FDR, so, please ignore the gseaplot generated by ssgsea. It's useless and misleading, therefore, fdr, and pval are not shown on the plot. If you'er seeking for ssGSEA with p-value output, please see here: https://github.com/broadinstitute/ssGSEA2.0
Actually, ssGSEA2.0 use the same method with GSEApy to calculate P-value, but FDR is not.
Q2: How to save plots using gseaplot, barplot, dotplot,heatmap in Jupyter?
A: e.g. gseaplot(...ofname='your.plot.pdf'). That's it
Q3: I want to use python 2 version of GSEApy.
A: See the docs here: https://gseapy.readthedocs.io/en/v0.9.4/index.html.
Q4: What cutoff do in like enrichr(), dotplot,barplot ?.
A: This argument only affects the final output figures, not the table of results.