GenMAPP is a free computer application for the PC designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web.

GenMAPP-CS is cross-platform program composed of multiple plugins within the program Cytoscape. GenMAPP-CS interfaces with WikiPathways to obtain pathways by reading the GPML format of these files. WikiPathways servers as the primary editor of pathways for GenMAPP-CS. GenMAPP-CS uses species gene databases built through through the BridgeDB project, which also provides databases for WikiPathways and PathVisio among other resources. GenMAPP-CS provides many of the same features as GenMAPP 2.0, with many additional and improved methods for gene and sub-gene analyses (e.g., GO-Elite, ClusterMaker, APT Affymetrix array normalization, GEO import advanced custom visualization methods and other methods available from Cytoscape plugins). GenMAPP-CS has an easy to use graphical user interface, designed for the bench lab biologist.