Question

Extending Gene Set Enrichment Analysis

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11.3 years ago

deschisandy ▴ 60

I have a set of enriched GO terms and would like to visualize them as a network using R. Maybe to to draw a DAG structure using as input the enriched GO terms.

I prefer not to use softwares as it requires the analysis to be done from the beginning.

r • 2.9k views

ADD COMMENT • link updated 11.3 years ago by Khader Shameer 18k • written 11.3 years ago by deschisandy ▴ 60

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Similar question? What's the best way to view and explore a large Gene Ontology DAG?

ADD REPLY • link 11.3 years ago by zx8754 12k

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Yes, I had seen this questionalready but the solutions were directed towards using softwares mostly which I would like to avoid. I wanted to do it with R

ADD REPLY • link 11.3 years ago by deschisandy ▴ 60

score 4 · Answer 1 · 2013-08-14

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11.3 years ago

Khader Shameer 18k

Have you tried REVIGO ? You can also create a gene-term network and weight them and visualize using Cytoscape or Gephi too.

ADD COMMENT • link 11.3 years ago by Khader Shameer 18k

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Yes, That is the only best option I have so far ! Thanks!

ADD REPLY • link 11.3 years ago by deschisandy ▴ 60