rvidal / fetchgeo

simple python script to download gene expression raw data files from NCBI's GEO (Gene expression omnibus)

fetchgeo

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Requirements

• Python 2.7+
• Biopython
• urllib2

Description

Downloads gene expression raw data from NCBI's Gene Expression Omnibus (GEO) Script runs in command line and takes two arguments:

• search query
• number of results to download

Usage

$ python fetchgeo.py 'ovarian cancer' 20

Output

Each result entries are downloaded & stored in a separately labelled folder containing:

• Raw Data
• SOFT file
• Text file containing detailed metadata for each study