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08-07-2014, 09:09 PM
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#1 |
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Member
Location: USA Join Date: Jul 2010
Posts: 58
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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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08-08-2014, 01:31 AM
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#2 |
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Member
Location: Belgium Join Date: Mar 2014
Posts: 22
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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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10-16-2014, 12:27 PM
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#3 | |
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Senior Member
Location: US Join Date: Aug 2013
Posts: 123
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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 Quote:
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