FAQ

Q : PiNGO aborts while parsing annotations, without any error message.

A : Check whether you have Java 1.6 installed. If not, install it. If yes, Cytoscape’s default memory settings are probably not sufficient. Try running Cytoscape from cytoscape.bat (Windows) or cytoscape.sh (Linux, Mac), or see here to increase Cytoscape’s default memory settings. On a laptop with 4GB RAM memory, setting Cytoscape’s VMOptions to -Xmx4GB -Xss10M should suffice to analyze genome-scale networks with tens of thousands of genes and hundreds of thousands to millions of edges.

Q : The default annotations/ontologies in PiNGO are outdated. I would like to use more recent annotations.

A : Download the most recent annotation and ontology files from the GO website. You can use these as custom annotation/ontology files.

 

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