NCBI Gene Expression Omnibus (GEO) support added to MetaPath

The NCBI Gene Expression Omnibus (GEO) is ‘is a public functional genomics data repository supporting MIAME-compliant data submissions.’ In other words, its a online database of freely available experimental gene-expression data. Quite useful.

To make this resource available to users of MetaPath I’ve today released a simple GEO-data import plugin. It currently supports SOFT-formatted dataset files. Support for family files is already implemented, but detection of what is what is on the todo list for now.

For the time being, here are a few screenshots/figures generated from this GEO dataset and analysis in action:

software/metapath/geo-demo-import.png

software/metapath/geo-demo-data.png

software/metapath/geo-demo-workflow.png

software/metapath/geo-demo-pca.png

Start to finish (without a prepared workflow): 18seconds.

The GEO import plugin is included in the default MetaPath distribution for download.


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