ReactomeFIViz GSEA

ReactomeFIViz is a Cytoscape app built upon Reactome pathways to help users perform pathway- and network-based data analysis and visualization. One of the most popular approaches to pathway analysis, which is an alternative to the traditional gene-list based pathway enrichment, is Gene Set Enrichment Analysis (GSEA). GSEA considers all genes with their scores based on a weighted Kolmogorov–Smirnov-like test and is a representative approach of second-generation pathway analysis. ReactomeFIViz implements features to perform GSEA analysis using Reactome pathways for a gene score file. 

More details about the GSEA feature and the ReactomeFIViz app can be found here