STAMP example datasets - Revision history

Dparks at 23:56, 25 May 2014

2014-05-25T23:56:57Z

2014-05-25T23:56:48Z

2014-05-25T23:46:42Z

2011-08-11T04:15:54Z

2011-08-11T04:15:42Z

2010-07-20T02:22:17Z

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2010-07-20T02:20:25Z

2010-01-14T16:46:37Z

2010-01-14T16:45:42Z

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 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]):

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-The following data sets were analyzed in ''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]):
+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: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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-'''Note''': additional datasets can be found in the ''examples'' folder of STAMP or downloaded [here|].
+'''Note''': additional datasets can be found in the ''examples'' folder of STAMP or downloaded [[Media:stamp_examples.zip|here]].

← Older revision		Revision as of 23:46, 25 May 2014
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−	~~STAMP is compatible with functional and taxonomic profiles generated by (see User's guide for details):~~	+	'''Note''': additional datasets can be found in the ''examples'' folder of STAMP or downloaded [here\|].
−
−	* [http://metagenomics.nmpdr.org/ MG-RAST]
−	* [http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=AbundanceProfiles&page=mergedForm IMG/M]
−
−
−	'''Note''': additional datasets can be found in the ''examples'' folder of STAMP.

← Older revision		Revision as of 04:15, 11 August 2011
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−	'''Note''': additional datasets can be found in the ~~<tt>~~examples~~</tt>~~ folder of STAMP.	+	'''Note''': additional datasets can be found in the ''examples'' folder of STAMP.

← Older revision		Revision as of 04:15, 11 August 2011
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−	'''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 <tt>examples</tt> folder of STAMP.

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 * [http://metagenomics.nmpdr.org/ MG-RAST]
-* [http://img.jgi.doe.gov/cgi-bin/m/main.cgi IMG/M]
+* [http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=AbundanceProfiles&page=mergedForm IMG/M]
 '''Note''': these data sets and others can be found in the <tt>examples</tt> folder of STAMP.

← Older revision		Revision as of 02:20, 20 July 2010
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−	The following data sets were analyzed in '''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]):	+	The following data sets were analyzed in ''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]):

	* [[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])

← Older revision		Revision as of 16:46, 14 January 2010
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−	The following data sets were analyzed in ''Identifying biologically important differences between pairs of metagenomic communities'' (Parks, DH and Beiko, RG, Bioinformatics, 2009 submitted):	+	The following data sets were analyzed in ''Identifying biologically important differences between pairs of metagenomic communities'' (Parks, D.H. and Beiko, R.G., Bioinformatics, 2009 submitted):

	* [[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])

← Older revision		Revision as of 16:45, 14 January 2010
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−	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 ''Identifying biologically important differences between pairs of metagenomic communities'' (Parks, DH and Beiko, RG, Bioinformatics, 2009 submitted):

	* [[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])