command-line pathway enrichment test

[sehrrot]

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

[Cytosine]

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.

[bigmw]

You can use gage package in R/Bioconductor for pathway, GO or gene set analysis:

http://bioconductor.org/packages/release/bioc/html/gage.html

gage has its own visualization functions (heatmap, scatterplot etc).
Pathway analysis results can be visualized using pathview

http://bioconductor.org/packages/release/bioc/html/pathview.html

The GAGE/Pathview workflow is ready for automated RNA-Seq (or microarray) pathway analysis:

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

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