Difference between revisions of "STAMP example datasets"

From Bioinformatics Software
Jump to navigationJump to search
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
The following data sets were analyzed in ''Identifying biologically important differences between pairs of metagenomic communities'' (Parks et al., Bioinformatics, submitted):  
+
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.]]
 +
 
 +
 
 +
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])
Line 7: Line 11:
 
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])
 
 
 
 
STAMP is compatible with functional and taxonomic profiles generated by (see User's guide for details):
 
 
 
* [http://metagenomics.nmpdr.org/ MG-RAST]
 
* [http://img.jgi.doe.gov/cgi-bin/m/main.cgi IMG/M]
 
  
  
'''Note''': these data sets and others can be found in the <tt>examples</tt> folder of STAMP.
+
'''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):


The User's guide makes use of the following data set:


Note: additional datasets can be found in the examples folder of STAMP or downloaded here.