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**Cytosine** · 08-08-2014, 01:31 AM

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** · 10-16-2014, 12:27 PM

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

gage

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

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

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

pathview

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

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

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

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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