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 (Statistical Analysis of Metagenomic Profiles) is a software package for analyzing metagenomic profiles (e.g., a taxonomic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) 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

• 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.
• Feb. 15, 2013: STAMP v2.0.0 (release candidate 5) released. Adds compatibility with MG-RAST LCA profiles.
• November 30, 2012: STAMP v2.0.0 (release candidate 4) released. Minor bug fixes (see version history for details).
• January 23, 2012: STAMP v2.0.0 (release candidate 3) released. Fixed generation of 'two groups' PCA plots along with various OS X related bugs.
• Previous announcements

Mailing list

• Join our mailing list to keep informed about STAMP developments.

Documentation

• Quick installation instructions (Microsoft Windows, Apple's Mac OS X, Linux, Command-line interface)
• User's Guide (v2.0.0)
• FAQs
• Version history

Downloads

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

• STAMP v2.0.0 (release candidate 6) executable for Microsoft Windows (~31MB)
• OS X and Linux 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