How to use deseq 2 file for keggscape in cytoscape
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3.3 years ago

Hello everyone, I have got deseq files for various datasets and have to analyze the pathways, I used genecodis web tool and had various pathways for a dataset, I want to shorten the number of pathways by using keggscape on cytoscape. But there are no tutorials covering this, same type of question has been posted in the forum but no replies to that too. Please let me know whether any tutorial are avaialble or in case it's not there , what are the steps or alternate methods I can do for that. Thank you in advance

RNA-SEQ Visualization Sequencing Cytoscape • 1.2k views
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have you managed to use this workflow you kindly mentioned? cheers

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2.4 years ago
eidriangm ▴ 60

Hi!

Within GeneCodis4 you can reduce the pathways obtained using the CoAnnotation analysis with the FPmax algorithm.

Additionally, there are tools that can handle functional enrichment results to sum them up and create interactive visualizations for you to display the terms that you find relevant to explain your experiment. For example for Gene Ontology results: http://revigo.irb.hr/

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Thanks a lot for your input, will check on it.

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