Dimont - Revision history

Keilwagen: /* DimontPredictor */

2017-01-17T08:49:48Z

DimontPredictor

← Older revision		Revision as of 08:49, 17 January 2017
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	The web-application of DimontPredictor is also installed at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].		The web-application of DimontPredictor is also installed at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].

			If you like to use the DimontPredictor with [http://www.jstacs.de/index.php/Slim Slim models], you need to download the [http://www.jstacs.de/downloads/SlimDimontPredictor.jar SlimDimontPredictor], which is currently only available as command line application.

	== DimontGenomeScan ==		== DimontGenomeScan ==

Keilwagen: /* DimontGenomeScan */

2017-01-17T08:32:34Z

DimontGenomeScan

← Older revision		Revision as of 08:32, 17 January 2017
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	In addition to the Dimont and DimontPredictor, we also provide a command line program for genomewide scans. This tool loads a Dimont model from the XML output of a previous Dimont run and a genome to be scanned in fastA format.		In addition to the Dimont and DimontPredictor, we also provide a command line program for genomewide scans. This tool loads a Dimont model from the XML output of a previous Dimont run and a genome to be scanned in fastA format.

	You can download the DimontGenomeScan as a [www.jstacs.de/downloads/DimontGenomeScan.jar Jar].		You can download the DimontGenomeScan as a [http://www.jstacs.de/downloads/DimontGenomeScan.jar Jar].

	== Installing the web-application ==		== Installing the web-application ==

Keilwagen at 08:31, 17 January 2017

2017-01-17T08:31:06Z

← Older revision		Revision as of 08:31, 17 January 2017
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	In addition to the Dimont and DimontPredictor, we also provide a command line program for genomewide scans. This tool loads a Dimont model from the XML output of a previous Dimont run and a genome to be scanned in fastA format.		In addition to the Dimont and DimontPredictor, we also provide a command line program for genomewide scans. This tool loads a Dimont model from the XML output of a previous Dimont run and a genome to be scanned in fastA format.

	You can download the DimontGenomeScan as a [~~http://~~www.jstacs.de/~~download.php?which=~~DimontGenomeScan.jar Jar].		You can download the DimontGenomeScan as a [www.jstacs.de/downloads/DimontGenomeScan.jar Jar].

	== Installing the web-application ==		== Installing the web-application ==

Keilwagen: DimontGenomeScan

2017-01-17T08:28:21Z

DimontGenomeScan

← Older revision		Revision as of 08:28, 17 January 2017
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	== Dimont @ Galaxy toolshed ==		== Dimont @ Galaxy toolshed ==

	Dimont, [[Dimont#DimontPredictor \|DimontPredictor]], and a [[Dimont#Data preparation\|data extraction]] tool are also available from the [http://toolshed.g2.bx.psu.edu Galaxy tool shed] in repository [http://toolshed.g2.bx.psu.edu/view/grau/dimont_motif_discovery dimont_motif_discovery]. From the toolshed, all tools can be installed with minimal effort from the Galaxy admin interface.		Dimont, [[Dimont#DimontPredictor\|DimontPredictor]], [[Dimont#DimontGenomeScan\|DimontGenomeScan]], and a [[Dimont#Data preparation\|data extraction]] tool are also available from the [http://toolshed.g2.bx.psu.edu Galaxy tool shed] in repository [http://toolshed.g2.bx.psu.edu/view/grau/dimont_motif_discovery dimont_motif_discovery]. From the toolshed, all tools can be installed with minimal effort from the Galaxy admin interface.

	== Dimont @ Chipster ==		== Dimont @ Chipster ==
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	If you use these data, please cite above publication and all appropriate original publications related to the data. In the archive, you find a ReadMe file containing the references to the original publications for each of the data sets.		If you use these data, please cite above publication and all appropriate original publications related to the data. In the archive, you find a ReadMe file containing the references to the original publications for each of the data sets.

	== ~~Dimont predictor~~ ==		== DimontPredictor ==
	In addition to the Dimont application, we also provide a command line program and a web-application of a prediction program that can be used to predict binding sites for motifs discovered by Dimont.		In addition to the Dimont application, we also provide a command line program and a web-application of a prediction program that can be used to predict binding sites for motifs discovered by Dimont in small (training or test) data sets.
	This tool loads a Dimont model from the XML output of a previous Dimont run. In addition to the input parameters explained above, you can specify a threshold on the p-value of predicted binding sites.		This tool loads a Dimont model from the XML output of a previous Dimont run. In addition to the input parameters explained above, you can specify a threshold on the p-value of predicted binding sites.
	DimontPredictor may be useful if you, for instance, want to predict binding sites of a previously discovered motifs in other data sets, or if you want to try different p-values for filtering predictions.		DimontPredictor may be useful if you, for instance, want to predict binding sites of a previously discovered motifs in other data sets, or if you want to try different p-values for filtering predictions.
			However, you should not use this tool for genomewide scans (cf. below).

	You can download Jars of the [http://www.jstacs.de/download.php?which=DimontPredictor command line program] and [http://www.jstacs.de/download.php?which=DimontPredictorWeb web-application] of DimontPredictor.		You can download Jars of the [http://www.jstacs.de/download.php?which=DimontPredictor command line program] and [http://www.jstacs.de/download.php?which=DimontPredictorWeb web-application] of DimontPredictor.

	The web-application of DimontPredictor is also installed at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].		The web-application of DimontPredictor is also installed at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].

			== DimontGenomeScan ==

			In addition to the Dimont and DimontPredictor, we also provide a command line program for genomewide scans. This tool loads a Dimont model from the XML output of a previous Dimont run and a genome to be scanned in fastA format.

			You can download the DimontGenomeScan as a [http://www.jstacs.de/download.php?which=DimontGenomeScan.jar Jar].

	== Installing the web-application ==		== Installing the web-application ==

Grau: /* Dimont @ Chipster */

2014-03-07T12:22:30Z

Dimont @ Chipster

← Older revision		Revision as of 12:22, 7 March 2014
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	== Dimont @ Chipster ==		== Dimont @ Chipster ==

	Dimont is also ~~included in~~ [http://chipster.csc.fi Chipster] starting from release 2.11.

			Dimont is also provided with [http://chipster.csc.fi Chipster] starting from Chipster release 2.11.

	== Download ==		== Download ==

Grau at 12:21, 7 March 2014

2014-03-07T12:21:11Z

← Older revision		Revision as of 12:21, 7 March 2014
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	Dimont, [[Dimont#DimontPredictor \|DimontPredictor]], and a [[Dimont#Data preparation\|data extraction]] tool are also available from the [http://toolshed.g2.bx.psu.edu Galaxy tool shed] in repository [http://toolshed.g2.bx.psu.edu/view/grau/dimont_motif_discovery dimont_motif_discovery]. From the toolshed, all tools can be installed with minimal effort from the Galaxy admin interface.		Dimont, [[Dimont#DimontPredictor \|DimontPredictor]], and a [[Dimont#Data preparation\|data extraction]] tool are also available from the [http://toolshed.g2.bx.psu.edu Galaxy tool shed] in repository [http://toolshed.g2.bx.psu.edu/view/grau/dimont_motif_discovery dimont_motif_discovery]. From the toolshed, all tools can be installed with minimal effort from the Galaxy admin interface.

			== Dimont @ Chipster ==

			Dimont is also included in [http://chipster.csc.fi Chipster] starting from release 2.11.

	== Download ==		== Download ==

Grau: /* Dimont @ Galaxy toolshed */

2013-11-20T09:43:53Z

Dimont @ Galaxy toolshed

← Older revision		Revision as of 09:43, 20 November 2013
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	== Dimont @ Galaxy toolshed ==		== Dimont @ Galaxy toolshed ==

	Dimont, DimontPredictor, and a data extraction tool are also available from the [http://toolshed.g2.bx.psu.edu Galaxy tool shed] in repository [http://toolshed.g2.bx.psu.edu/view/grau/dimont_motif_discovery dimont_motif_discovery]. From the toolshed, all tools can be installed with minimal effort from the Galaxy admin interface.		Dimont, [[Dimont#DimontPredictor \|DimontPredictor]], and a [[Dimont#Data preparation\|data extraction]] tool are also available from the [http://toolshed.g2.bx.psu.edu Galaxy tool shed] in repository [http://toolshed.g2.bx.psu.edu/view/grau/dimont_motif_discovery dimont_motif_discovery]. From the toolshed, all tools can be installed with minimal effort from the Galaxy admin interface.

	== Download ==		== Download ==

Grau at 09:41, 20 November 2013

2013-11-20T09:41:53Z

← Older revision		Revision as of 09:41, 20 November 2013
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	== Dimont web-server ==		== Dimont web-server ==
	Dimont is available as a public web-server at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].		Dimont is available as a public web-server at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].

			== Dimont @ Galaxy toolshed ==

			Dimont, DimontPredictor, and a data extraction tool are also available from the [http://toolshed.g2.bx.psu.edu Galaxy tool shed] in repository [http://toolshed.g2.bx.psu.edu/view/grau/dimont_motif_discovery dimont_motif_discovery]. From the toolshed, all tools can be installed with minimal effort from the Galaxy admin interface.

	== Download ==		== Download ==

Grau: /* Paper */

2013-11-20T09:25:58Z

Paper

← Older revision		Revision as of 09:25, 20 November 2013
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	If you use Dimont, please cite		If you use Dimont, please cite

	J. Grau, S. Posch, I. Grosse, and J. Keilwagen. [http://nar.oxfordjournals.org/content/early/2013/09/19/nar.gkt831 A general approach for discriminative de-novo motif discovery from high-throughput data]. ''Nucleic Acids Research'', 2013. doi:		J. Grau, S. Posch, I. Grosse, and J. Keilwagen. [http://nar.oxfordjournals.org/content/early/2013/09/19/nar.gkt831 A general approach for discriminative de-novo motif discovery from high-throughput data]. ''Nucleic Acids Research'', 41(21):e197, 2013. doi:
	10.1093/nar/gkt831		10.1093/nar/gkt831

Grau: /* Paper */

2013-09-21T14:15:44Z

Paper

← Older revision		Revision as of 14:15, 21 September 2013
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	If you use Dimont, please cite		If you use Dimont, please cite

	J. Grau, S. Posch, I. Grosse, and J. Keilwagen. A general approach for discriminative de-novo motif discovery from high-throughput data. ''Nucleic Acids Research'', 2013. doi:		J. Grau, S. Posch, I. Grosse, and J. Keilwagen. [http://nar.oxfordjournals.org/content/early/2013/09/19/nar.gkt831 A general approach for discriminative de-novo motif discovery from high-throughput data]. ''Nucleic Acids Research'', 2013. doi:
	10.1093/nar/gkt831		10.1093/nar/gkt831