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Old 08-07-2014, 09:09 PM   #1
sehrrot
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Default command-line pathway enrichment test

Hi

I have been doing pathway analyses using Cytoscape Cluego but now I have many input files. Is there any command line tool for pathway enrichment test (e.g. KEGG, GO, REACTOME etc)?

Thanks
Chris
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Old 08-08-2014, 01:31 AM   #2
Cytosine
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You could have a go with R and it's packages for pathway enrichment tests (e.g. GOStats or topGO).

If you have a lot of input files, then scripting such a task like will make your life a lot easier.
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Old 10-16-2014, 12:27 PM   #3
bigmw
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You can use gage package in R/Bioconductor for pathway, GO or gene set analysis:
http://bioconductor.org/packages/rel...html/gage.html

gage has its own visualization functions (heatmap, scatterplot etc).
Pathway analysis results can be visualized using pathview
http://bioconductor.org/packages/rel.../pathview.html

The GAGE/Pathview workflow is ready for automated RNA-Seq (or microarray) pathway analysis:
http://bioconductor.org/packages/rel...eqWorkflow.pdf


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Originally Posted by sehrrot View Post
Hi

I have been doing pathway analyses using Cytoscape Cluego but now I have many input files. Is there any command line tool for pathway enrichment test (e.g. KEGG, GO, REACTOME etc)?

Thanks
Chris
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