STAMP

Using STAMP to identify SEED subsystems which are differentially abundant in a pair of iron mine metagenomes (data original described in Edwards et al., 2006).

STAMP (Statistical analysis of metagenomic profiles) is a software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevancy of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.

Documentation

• Quick installation instructions
• User's Guide
• FAQs

Downloads

• STAMP v1.0 executable [Windows] [OS X]
• STAMP v1.0 Python [source code]

Examples

• Image gallery
• Example datasets

Citing STAMP

If you use STAMP in your research, please cite:

Parks, D.H. and Beiko, R.G. Identifying biologically important differences between pairs of metagenomic communities. Submitted to Bioinformatics on Dec. XX, 2009.

Contact Information

STAMP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Donovan Parks (parks [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.

Funding for STAMP

The development and deployment of STAMP has been supported by several organizations:

• Genome Atlantic
• The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the Tula Foundation
• The Natural Sciences and Engineering Research Council of Canada
• The Dalhousie Faculty of Computer Science