Difference between revisions of "STAMP"

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[[Image:STAMP2_EBPR_Aphosphatis_ExtendedErrorBar.png|thumb|right|500px|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 [http://www.ncbi.nlm.nih.gov/pubmed/20130030 Parks and Beiko, 2010]).]]
 
[[Image:STAMP2_EBPR_Aphosphatis_ExtendedErrorBar.png|thumb|right|500px|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 [http://www.ncbi.nlm.nih.gov/pubmed/20130030 Parks and Beiko, 2010]).]]
  
STAMP ('''St'''atistical '''A'''nalysis of '''M'''etagenomic '''P'''rofiles) 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.
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STAMP is a software package for analyzing taxonomic or metabolic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. Statistical hypothesis tests for pairs of samples or groups of samples is support along with a wide range of exploratory plots. STAMP 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 ===
 
=== Announcements ===
  
* Mar. 6, 2014: STAMP v2.0.2 released. Adds support for BIOM profiles including those generated by [http://picrust.github.io/picrust/ PICRUSt] and [http://qiime.org/ QIIME].
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* June 26, 2015: STAMP v2.1.3 released. Minor bug fix to scatter plot to properly handle profiles contained a single feature.
* 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.
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* June 15, 2015: STAMP v2.1.2 released. Minor enhancements to extended error bar, heatmap, and profile bar plots.
* Sept. 2, 2013: OS X user may be experiencing problems running STAMP due to a bug in the latest version of matplotlib. Click [[matplotlib bug on OS X|here]] for details.
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* June 7, 2015: STAMP v2.1.1 released. Resolves issue with v2.1.0 installation.
* May 24, 2012: STAMP v2.0.0 (release candidate 6) released. Improved handling of degenerate cases and unclassified taxa in STAMP profiles.
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* June 4, 2015: STAMP v2.1.0 released. Resolves the _hierarchy_wrap issue. Requires numpy >= 1.9.1, scipy >= 0.15.1, matplotlib >= 1.4.2.
 
* [[Previous announcements]]
 
* [[Previous announcements]]
 
=== Mailing list ===
 
 
* Join our [http://ratite.cs.dal.ca/software_email_list/subscribe mailing list] to keep informed about STAMP developments.
 
  
 
=== Documentation ===
 
=== Documentation ===
* [[Quick installation instructions for STAMP|Quick installation instructions]] (Microsoft Windows, Apple's Mac OS X, Linux, Command-line interface)
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* [[Quick installation instructions for STAMP|Quick installation instructions]] (Microsoft Windows, Linux, Apple's Mac OS X)
* [https://github.com/dparks1134/STAMP/blob/master/manual/STAMP_Users_Guide.pdf|User's Guide]
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* [[Media:STAMP_Users_Guide.zip|User's Guide]]
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* [https://groups.google.com/forum/?hl=en#!forum/stamp_help Google Group]
 
* [[STAMP FAQs|FAQs]]
 
* [[STAMP FAQs|FAQs]]
 
* [[STAMP version history|Version history]]
 
* [[STAMP version history|Version history]]
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''Please uninstall previous versions of STAMP before installing a new release.''
 
''Please uninstall previous versions of STAMP before installing a new release.''
  
* [https://github.com/dparks1134/STAMP/releases/download/v2.0.2/STAMP_2_0_2-windows.exe STAMP v2.0.2] setup package for Microsoft Windows (~35MB)
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* [https://github.com/dparks1134/STAMP/releases/download/v2.1.3/STAMP_2_1_3.exe STAMP v2.1.3] setup package for Microsoft Windows (~42MB)
* OS X and Linux users can follow the instructions to [[Quick installation instructions for STAMP|install from source]]
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* Linux and OS X users can follow the instructions to [[Quick installation instructions for STAMP|install from source]]
 
* [https://github.com/dparks1134/STAMP STAMP GitHub Repository]
 
* [https://github.com/dparks1134/STAMP STAMP GitHub Repository]
 
* [[Previous versions|Previous versions]]
 
* [[Previous versions|Previous versions]]
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=== Additional Scripts ===
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* [[Media:CheckHierarchy.zip|checkHierarchy.py]]: identify entries within a STAMP profile that are not strictly hierarchical
  
 
=== Examples ===
 
=== Examples ===
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== Citing STAMP ==
 
== Citing STAMP ==
  
If you use STAMP in your research, please cite:
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If you use STAMP v2+ in your research, we appreciate you citing:
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* Parks DH, Tyson GW, Hugenholtz P, Beiko RG. (2014). [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btu494?ijkey=T0tIsUilyLV0x3w&keytype=ref STAMP: Statistical analysis of taxonomic and functional profiles]. ''Bioinformatics'', 30, 3123-3124.
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STAMP v1 manuscript:
  
'''Parks, D.H. and Beiko, R.G. (2010). Identifying biologically relevant differences between metagenomic communities. ''Bioinformatics'', 26, 715-721.''' ([http://bioinformatics.oxfordjournals.org/cgi/content/short/26/6/715 Abstract])
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* Parks DH and Beiko RG. (2010). [http://bioinformatics.oxfordjournals.org/cgi/content/short/26/6/715 Identifying biologically relevant differences between metagenomic communities]. ''Bioinformatics'', 26, 715-721.
  
 
== Contact Information ==
 
== 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.  
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STAMP is in active development and we are interested in discussing all potential applications of this software. We recommend you send suggestions, comments, and bug reports to the [[https://groups.google.com/forum/?hl=en#!forum/stamp_help STAMP Google Group]] so all commuity members can participate and benefit from the discussions. 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. If you need to contact the authors of STAMP privately, please email Rob Beiko (beiko [at] cs.dal.ca). 
  
 
== Funding ==
 
== Funding ==

Latest revision as of 01:44, 26 June 2015

StampIcon.png
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. Statistical hypothesis tests for pairs of samples or groups of samples is support along with a wide range of exploratory plots. STAMP 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 26, 2015: STAMP v2.1.3 released. Minor bug fix to scatter plot to properly handle profiles contained a single feature.
  • June 15, 2015: STAMP v2.1.2 released. Minor enhancements to extended error bar, heatmap, and profile bar plots.
  • June 7, 2015: STAMP v2.1.1 released. Resolves issue with v2.1.0 installation.
  • June 4, 2015: STAMP v2.1.0 released. Resolves the _hierarchy_wrap issue. Requires numpy >= 1.9.1, scipy >= 0.15.1, matplotlib >= 1.4.2.
  • Previous announcements

Documentation

Downloads

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

Additional Scripts

  • checkHierarchy.py: identify entries within a STAMP profile that are not strictly hierarchical

Examples

Citing STAMP

If you use STAMP v2+ in your research, we appreciate you citing:


STAMP v1 manuscript:

Contact Information

STAMP is in active development and we are interested in discussing all potential applications of this software. We recommend you send suggestions, comments, and bug reports to the [STAMP Google Group] so all commuity members can participate and benefit from the discussions. 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. If you need to contact the authors of STAMP privately, please email Rob Beiko (beiko [at] cs.dal.ca).

Funding

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