STAMP

Using STAMP to identify SEED subsystems which are differentially abundant between Candidatus Accumulibacter phosphatis sequences obtained from a pair of enhanced biological phosphorus removal (EBPR) sludge metagenomes(data originally described in Parks and Beiko, 2010).

STAMP is a software package for analyzing taxonomic or metabolic 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 relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.

Announcements

• June 18, 2014: STAMP v2.0.4 released. Migrated to BIOM v2 format.
• May 24, 2014: STAMP v2.0.3 released. Better support for installation under Ubuntu.
• Mar. 6, 2014: STAMP v2.0.2 released. Adds support for BIOM profiles including those generated by PICRUSt and QIIME.
• Feb. 9, 2014: STAMP v2.0.1 released. Adds heatmap plot. Fixes bug in multi-group plots causing DP values to be scaled by an 100.
• Sept. 2, 2013: OS X user may be experiencing problems running STAMP due to a bug in the latest version of matplotlib. Click here for details.
• May 24, 2012: STAMP v2.0.0 (release candidate 6) released. Improved handling of degenerate cases and unclassified taxa in STAMP profiles.
• Previous announcements

Documentation

• Quick installation instructions (Microsoft Windows, Linux, Apple's Mac OS X)
• User's Guide
• FAQs
• Version history

Downloads

Please uninstall previous versions of STAMP before installing a new release.

• STAMP v2.0.4 setup package for Microsoft Windows (~39MB)
• Linux and OS X users can follow the instructions to install from source
• STAMP GitHub Repository
• Previous versions

Examples

• Image gallery
• Example datasets

Citing STAMP

If you use STAMP in your research, please cite:

Parks, D.H. and Beiko, R.G. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-721. (Abstract)

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 Rob Beiko (beiko [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

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
• Killam Trust
• The Natural Sciences and Engineering Research Council of Canada
• The Dalhousie Faculty of Computer Science