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  • sehrrot
    Member
    • Jul 2010
    • 58
    #1

    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
    Tags: None
  • Cytosine
    Member
    • Mar 2014
    • 22
    #2
    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.

    Comment

    • bigmw
      Senior Member
      • Aug 2013
      • 124
      #3
      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

      Comment

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