Does anyone know how to import/read/load the results of the gene set enrichment analysis generated from the GSEA software into R? I want to visualize the results, plot them and create heatmaps in R using ggplot, clusterprofiler, etc.
Your results from the GSEA software will be stored in two files called gsea_report_for_na_pos_12345.tsv and gsea_report_for_na_neg_12345.tsv in whatever folder you selected as your output folder when using the software. To load into R you can use:
(You also mention you want to use clusterprofiler to visualise the results - I tried to replot results of the Broad's GSEA software with clusterprofiler with no luck, it might not be possible, see this post: be great if someone could prove me wrong here.)