PINBPA (Protein interaction network-based pathway analysis) for genome-wide association studies (GWAS) has been developed as a Cytoscape app, to enable analysis of GWAS data in a network fashion.
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PINBPA: Cytoscape app for network analysis of GWAS data.
Wang L, Matsushita T, Madireddy L, Mousavi P, Baranzini S.
Bioinformatics. 2014 Sep 25. pii: btu644