Software (Cytoscape and EnrichmentMap) version not match to the protocol, difficult to follow

Question

[lilianbo2003]

Software (Cytoscape and EnrichmentMap) version not match to the protocol, difficult to follow

I am trying to follow the steps in the Nature Protocols （volume 14, pages482–517(2019) Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap）to analysis my data using EnrichmentMap in the Cytoscape. But the version of I am currently downloaded is Cytoscape 3.8.2 and EnrichmentMap 3.3.1 , In the paper, the Cytoscape is v.3.6.0 and EnrichmentMap 3.0. some discriptions in the article were hard to follow.

As a new learner, I notice the buttons in the paper could not match the software. Is there a updated protocol or I can download the early version of those two software.

Thank you! Lianbo

Answer 1

[Mensur Dlakic]

Using more recent versions of programs is typically not a problem, but you can verify that directly with the authors. As to older versions that match the article, usually there are links on the download page to fetch older versions - you just need to look for them.

• http://chianti.ucsd.edu/cytoscape-3.6.0/
• https://github.com/BaderLab/EnrichmentMapApp/releases/tag/v3.0.0

Answer 2

[ruth.isserlin]

There have been many updates in the software tools associated with the protocol. I have made an updated protocol where I hope I caught all the changes. You can find it here: https://baderlab.github.io/EnrichmentMap_Protocol/