Difference between revisions of "STAMP"

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__NOTOC__
 
__NOTOC__
 
[[Image:StampIcon.png|left]]
 
[[Image:StampIcon.png|left]]
[[Image:RumenErrorBarPlot.png|thumb|right|500px|Using STAMP to identify SEED subsystems which are differentially abundant in a pair of bovine rumen microbiomes (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/19181843 Brulc et al., 2009]).]]
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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]).]]
  
STAMP ('''St'''atistical '''A'''nalysis of '''M'''etagenomic '''P'''rofiles) is a software package for analyzing metagenomic profiles (e.g., a phylogenetic 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.
 
 
=== STAMP v2.0.0 - BETA ===
 
 
 
STAMP v2.0.0 is in active development. It provides support for comparing multiple groups of metagenomic samples (i.e. ANOVA, post-hoc tests, t-test) along with a number of other additional features. We expect to release it by the end of August. Join the STAMP [http://ratite.cs.dal.ca/software_email_list/subscribe mailing list] if you wish to be updated on STAMP developments.
 
 
 
Windows users can try out a BETA version of STAMP v2.0.0. There are still some known bugs, but the program is stable. This is also your chance to suggest new features! To get started, try out the example data in /examples/EnterotypesArumugam.
 
 
 
* [[Media:STAMP_2_Beta_Setup_r10.exe|STAMP v2.0.0 (BETA - release 10) for Windows]] (released August 8, 2011)
 
* [[Media:STAMP_2_Beta_Setup_r10_source.zip|Stamp v2.0.0 (BETA - release 10) source code]]
 
 
 
''Please uninstall any previous versions of STAMP before installing the above BETA release.''
 
  
 
=== Announcements ===
 
=== Announcements ===
  
* Apr. 7, 2011: Patch for STAMP v1.08 released. This patch provides improved support for converting MG-RAST v3.0 profiles into STAMP profiles.
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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.
* Mar. 14, 2011: STAMP v1.08 released. Minor update to provides support for the latest [http://metagenomics.anl.gov/ MG-RAST] profiles.
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* June 15, 2015: STAMP v2.1.2 released. Minor enhancements to extended error bar, heatmap, and profile bar plots.
* Sept. 7, 2010: STAMP v1.07 released. Improved scatter plots, enhanced annotation of COG profiles, and minor bug fixes.
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* 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]]
 
* [[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)
* [[Media:STAMP_Users_Guide.pdf|User's Guide (v1.08)]]
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* [[Media:STAMP_Users_Guide.zip|User's Guide]]
 +
* [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]]
  
 
=== Downloads ===
 
=== Downloads ===
* [[STAMP v1.08.1 patch|STAMP v1.08.1 patch]]: provides improved support for converting MG-RAST v3.0 profiles into STAMP profiles.
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''Please uninstall previous versions of STAMP before installing a new release.''
* [[Media:STAMP_1.08_Setup.exe|STAMP v1.08 executable]] for Microsoft Windows (~18MB)
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* [[Media:STAMP_1_08_OS_X.zip‎|STAMP v1.08 executable]] for Mac OS X Leopard and Snow Leopard (~73MB)
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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)
* [[Media:STAMP_1_08_source.zip|STAMP v1.08 source code]] (~2MB)
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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]
 
* [[Previous versions|Previous versions]]
 
* [[Previous versions|Previous versions]]
 +
 +
=== 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:
 +
 
 +
* 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.
 +
 
 +
 
 +
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 ==
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* [http://www.genomeatlantic.ca Genome Atlantic]
 
* [http://www.genomeatlantic.ca Genome Atlantic]
 
* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]
 
* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]
 +
* [http://www.killamtrusts.ca/ Killam Trust]
 
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]
 
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]
 
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]
 
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]

Latest revision as of 04:44, 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: