We have been tasked with performing Gene Set Enrichment Analysis (GSEA) on GEO datasets as part of our masters project. These results should then be visualised as Heatmaps or even interaction networks.
The problems we are having is with finding appropriate R packages to do this. Ones that seem like they could be useful are the gage, gageData and pathview pacakages but these seem to perform Generally Applicable Gene-set Enrichment (GAGE).
What are the differences between GSEA and GAGE analyses? Would it be substitute one for the other? Are there any simple to use packages that will allow us to perform these analyses on GEO datasets and visualise the results?