Difference between revisions of "STAMP example datasets"
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| − | The following data sets were analyzed in ''Identifying biologically | + | The following data sets were analyzed in ''Parks, DH, Tyson GW, Hugenholtz P, Beiko RG. (2014). STAMP: Statistical analysis of taxonomic and functional profiles. Submitted to Bioinformatics in June, 2014.'': |
| + | * [[Media:stamp2_examples.zip|Taxonomic profiles of coal seam gas communities and COG profiles for Cyanobacterial genomes.]] | ||
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| + | The following data sets were analyzed in ''Parks, DH and Beiko, RG. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-721.'' ([http://bioinformatics.oxfordjournals.org/cgi/content/short/26/6/715 Abstract]): | ||
* [[Media:RedBlack.spf|SEED functional profile for Soudin iron mine metagenomes]] (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/16549033 Edwards et al., 2006]) | * [[Media:RedBlack.spf|SEED functional profile for Soudin iron mine metagenomes]] (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/16549033 Edwards et al., 2006]) | ||
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The User's guide makes use of the following data set: | The User's guide makes use of the following data set: | ||
| − | * [[Media:MouseTurnbaughMG-RAST_Functional.spf|SEED taxonomic profile for an obese and lean mouse microbiome]] (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/17183312 Turnbaugh et al., 2006]) | + | * [[Media:MouseTurnbaughMG-RAST_Functional.spf|SEED taxonomic profile for an obese and a lean mouse microbiome]] (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/17183312 Turnbaugh et al., 2006]) |
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| − | '''Note''': | + | '''Note''': additional datasets can be found in the ''examples'' folder of STAMP or downloaded [[Media:stamp_examples.zip|here]]. |
Latest revision as of 23:56, 25 May 2014
The following data sets were analyzed in Parks, DH, Tyson GW, Hugenholtz P, Beiko RG. (2014). STAMP: Statistical analysis of taxonomic and functional profiles. Submitted to Bioinformatics in June, 2014.:
The following data sets were analyzed in Parks, DH and Beiko, RG. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-721. (Abstract):
- SEED functional profile for Soudin iron mine metagenomes (data originally described in Edwards et al., 2006)
- SEED functional profile for Candidatus Accumulibacter phosphatis (data originally described in Martín et al., 2006)
The User's guide makes use of the following data set:
- SEED taxonomic profile for an obese and a lean mouse microbiome (data originally described in Turnbaugh et al., 2006)
Note: additional datasets can be found in the examples folder of STAMP or downloaded here.
