gCMAPWeb-package: A web-interface for gene-set enrichment analysis
In gCMAPWeb: A web interface for gene-set enrichment analyses

Description Details Author(s) References Examples

A web-interface for gene-set enrichment analysis

This package provides a stand-alone web interface for gene-set enrichment analysis. Run either through R's internal Rhttpd server of deployed through an Apache2 webserver, gCMAPWeb allows users to search reference datasets stored in NChannelSet or CMAPCollection objects via three different methods:

Directional queries performed by calculating the parametric JG score from the reference datasets
Non-directional queries performed via Fisher's exact test
Profile queires performed by calculating the parametric JG score from the query data

A web interace is populated based on a configuration file in YAML format and additional information from the reference dataset objects (if available). For each query, a report is generated in html format, including graphs and tabular output. Extensive customization of the graphical user interface can easily be performed through global options.

Thomas Sandmann

Jiang Z, Gentleman R., Extensions to gene set enrichment. Bioinformatics. 2007 Feb 1;23(3):306-13 http://www.ncbi.nlm.nih.gov/pubmed/17127676

1	example( gCMAPWeb )

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gCMAPW> if (interactive()) {
gCMAPW+   ## start a gCMAPWeb instance with the example data and
gCMAPW+   ## configuration provided in the package
gCMAPW+   gCMAPWeb()
gCMAPW+   ## same as above, explicitely specifying the location
gCMAPW+   ## of the configuration file
gCMAPW+   gCMAPWeb( 
gCMAPW+     config.file.path = system.file("config", "config.yml", 
gCMAPW+                                     package = "gCMAPWeb" )
gCMAPW+   )
gCMAPW+ }
Warning message:
system call failed: Cannot allocate memory