STAMP: statistical analysis of taxonomic and functional profiles

Donovan H Parks; Gene W Tyson; Philip Hugenholtz; Robert G Beiko

doi:10.1093/bioinformatics/btu494

STAMP: statistical analysis of taxonomic and functional profiles

Bioinformatics. 2014 Nov 1;30(21):3123-4. doi: 10.1093/bioinformatics/btu494. Epub 2014 Jul 23.

Authors

Donovan H Parks¹, Gene W Tyson², Philip Hugenholtz², Robert G Beiko¹

Affiliations

¹ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Advanced Water Management Centre, The University of Queensland, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia and Dalhousie University, Halifax, Nova Scotia, Canada.
² Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Advanced Water Management Centre, The University of Queensland, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia and Dalhousie University, Halifax, Nova Scotia, Canada Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Advanced Water Management Centre, The University of Queensland, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia and Dalhousie University, Halifax, Nova Scotia, Canada.

Abstract

STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles. It supports tests for comparing pairs of samples or samples organized into two or more treatment groups. Effect sizes and confidence intervals are provided to allow critical assessment of the biological relevancy of test results. A user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots.

Availability and implementation: STAMP is licensed under the GNU GPL. Python source code and binaries are available from our website at: http://kiwi.cs.dal.ca/Software/STAMP.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteria / classification*
Classification / methods
Confidence Intervals
Cyanobacteria / classification
Cyanobacteria / genetics
Data Interpretation, Statistical
Genome, Bacterial
Humans
Software*