Main Page - Revision history

Grau: /* Latest Papers */

2019-02-23T22:58:01Z

Latest Papers

← Older revision		Revision as of 22:58, 23 February 2019
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	== Latest Papers ==		== Latest Papers ==
			The paper '''''[[Catchitt \| Accurate prediction of cell type-specific transcription factor binding]]''''' has been published in [https://doi.org/10.1186/s13059-018-1614-y Genome Biology].

	The paper '''''[[PCTLearn \| Algorithms for learning parsimonious context trees]]''''' has been published in [https://link.springer.com/article/10.1007/s10994-018-5770-9 Machine Learning].		The paper '''''[[PCTLearn \| Algorithms for learning parsimonious context trees]]''''' has been published in [https://link.springer.com/article/10.1007/s10994-018-5770-9 Machine Learning].

Eggeling: /* Applications */

2018-11-13T16:23:06Z

Applications

← Older revision		Revision as of 16:23, 13 November 2018
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	* [[AnnoTALE]]		* [[AnnoTALE]]
	* [[InMoDe]]		* [[InMoDe]]
			* [[Disentangler]]

	== Bug reports & Feature requests ==		== Bug reports & Feature requests ==

Eggeling: /* Latest Papers */

2018-11-13T15:48:04Z

Latest Papers

← Older revision		Revision as of 15:48, 13 November 2018
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	== Latest Papers ==		== Latest Papers ==
			The paper '''''[[PCTLearn \| Algorithms for learning parsimonious context trees]]''''' has been published in [https://link.springer.com/article/10.1007/s10994-018-5770-9 Machine Learning].

	The paper '''''[[Disentangler \| Disentangling transcription factor binding site complexity]]''''' has been published in [https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky683/5063190 Nucleic Acids Research].		The paper '''''[[Disentangler \| Disentangling transcription factor binding site complexity]]''''' has been published in [https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky683/5063190 Nucleic Acids Research].

Grau: /* Current release */

2018-11-09T15:30:21Z

Current release

← Older revision		Revision as of 15:30, 9 November 2018
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	''You find an overview of the new features in the [[Version history]].''<br />		''You find an overview of the new features in the [[Version history]].''<br />
	We also provide an [http://www.jstacs.de/api/index.html API documentation], a [[Cookbook]], and a [http://www.jstacs.de/downloads/refcard.pdf Reference card] for this release.		We also provide an [http://www.jstacs.de/api/index.html API documentation], a [[Cookbook]], and a [http://www.jstacs.de/downloads/refcard.pdf Reference card] for this release.

			The current Jstacs code, including changes made since the last release, is available from [https://github.com/Jstacs github].

	== Getting started & Cookbook==		== Getting started & Cookbook==

Eggeling: /* Latest Papers */

2018-08-02T07:06:30Z

Latest Papers

← Older revision		Revision as of 07:06, 2 August 2018
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	== Latest Papers ==		== Latest Papers ==
			The paper '''''[[Disentangler \| Disentangling transcription factor binding site complexity]]''''' has been published in [https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky683/5063190 Nucleic Acids Research].

	The paper '''''[[GeMoMa \| Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi]]''''' has been published in [https://link.springer.com/article/10.1186%2Fs12859-018-2203-5 BMC Bioinformatics].		The paper '''''[[GeMoMa \| Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi]]''''' has been published in [https://link.springer.com/article/10.1186%2Fs12859-018-2203-5 BMC Bioinformatics].

Keilwagen: /* Latest Papers */

2018-06-13T07:56:43Z

Latest Papers

← Older revision		Revision as of 07:56, 13 June 2018
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	== Latest Papers ==		== Latest Papers ==
			The paper '''''[[GeMoMa \| Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi]]''''' has been published in [https://link.springer.com/article/10.1186%2Fs12859-018-2203-5 BMC Bioinformatics].

	The paper '''''[[InMoDe \| InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites]]''''' has been published in [https://academic.oup.com/bioinformatics/article/33/4/580/2666342/InMoDe-tools-for-learning-and-visualizing-intra Bioinformatics].		The paper '''''[[InMoDe \| InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites]]''''' has been published in [https://academic.oup.com/bioinformatics/article/33/4/580/2666342/InMoDe-tools-for-learning-and-visualizing-intra Bioinformatics].

	The paper '''''[[AnnoTALE \| AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences]]''''' has been published in [http://www.nature.com/articles/srep21077 Scientific Reports].		The paper '''''[[AnnoTALE \| AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences]]''''' has been published in [http://www.nature.com/articles/srep21077 Scientific Reports].

	The paper '''''[[GeMoMa \| Using intron position conservation for homology-based gene predictions]]''''' has been published in [https://nar.oxfordjournals.org/content/early/2016/02/17/nar.gkw092 Nucleic Acids Research].

	The paper '''''[[PMMdeNovo \| Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data ]]''''' has been published in [http://www.biomedcentral.com/1471-2105/16/375 BMC Bioinformatics].		The paper '''''[[PMMdeNovo \| Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data ]]''''' has been published in [http://www.biomedcentral.com/1471-2105/16/375 BMC Bioinformatics].

Grau: /* JstacsFX */

2017-09-08T16:07:20Z

JstacsFX

← Older revision		Revision as of 16:07, 8 September 2017
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	JstacsFX is a library for building applications with graphical user interface based on Jstacs classes and using JavaFX. JstacsFX builds upon the [http://www.jstacs.de/api/de/jstacs/tools/JstacsTool.html JstacsTool] interface that has also been used to create [http://www.jstacs.de/api-2.3/de/jstacs/tools/ui/cli/CLI.html command line] and [http://www.jstacs.de/api-2.3/de/jstacs/tools/ui/galaxy/Galaxy.html Galaxy] versions of tools with minimal effort. In addition it makes use of the [http://www.jstacs.de/api-2.3/de/jstacs/parameters/Parameter.html Parameter], [http://www.jstacs.de/api-2.3/de/jstacs/results/Result.html Result], and [http://www.jstacs.de/api-2.3/de/jstacs/results/savers/ResultSaver.html ResultSaver] classes of Jstacs.		JstacsFX is a library for building applications with graphical user interface based on Jstacs classes and using JavaFX. JstacsFX builds upon the [http://www.jstacs.de/api/de/jstacs/tools/JstacsTool.html JstacsTool] interface that has also been used to create [http://www.jstacs.de/api-2.3/de/jstacs/tools/ui/cli/CLI.html command line] and [http://www.jstacs.de/api-2.3/de/jstacs/tools/ui/galaxy/Galaxy.html Galaxy] versions of tools with minimal effort. In addition it makes use of the [http://www.jstacs.de/api-2.3/de/jstacs/parameters/Parameter.html Parameter], [http://www.jstacs.de/api-2.3/de/jstacs/results/Result.html Result], and [http://www.jstacs.de/api-2.3/de/jstacs/results/savers/ResultSaver.html ResultSaver] classes of Jstacs.

	The current release of JstacsFX is available from [[Downloads ~~\| here~~]] and an [http://www.jstacs.de/api-fx/index.html API documentation] is available.		The current release of JstacsFX is available from [[Downloads]] and an [http://www.jstacs.de/api-fx/index.html API documentation] is available.

	Example applications using JstacsFX for their graphical user interface are [[InMoDe]] and [[AnnoTALE]].		Example applications using JstacsFX for their graphical user interface are [[InMoDe]] and [[AnnoTALE]].

Grau: /* JstacsFX */

2017-09-08T15:42:10Z

JstacsFX

← Older revision		Revision as of 15:42, 8 September 2017
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	== JstacsFX ==		== JstacsFX ==
	JstacsFX is a library for building applications with graphical user interface based on Jstacs classes and using JavaFX.		JstacsFX is a library for building applications with graphical user interface based on Jstacs classes and using JavaFX. JstacsFX builds upon the [http://www.jstacs.de/api/de/jstacs/tools/JstacsTool.html JstacsTool] interface that has also been used to create [http://www.jstacs.de/api-2.3/de/jstacs/tools/ui/cli/CLI.html command line] and [http://www.jstacs.de/api-2.3/de/jstacs/tools/ui/galaxy/Galaxy.html Galaxy] versions of tools with minimal effort. In addition it makes use of the [http://www.jstacs.de/api-2.3/de/jstacs/parameters/Parameter.html Parameter], [http://www.jstacs.de/api-2.3/de/jstacs/results/Result.html Result], and [http://www.jstacs.de/api-2.3/de/jstacs/results/savers/ResultSaver.html ResultSaver] classes of Jstacs.

	The current release of JstacsFX is available from [[Downloads \| here]] and an [http://www.jstacs.de/api-fx/index.html API documentation] is available.		The current release of JstacsFX is available from [[Downloads \| here]] and an [http://www.jstacs.de/api-fx/index.html API documentation] is available.

Grau at 15:35, 8 September 2017

2017-09-08T15:35:48Z

← Older revision		Revision as of 15:35, 8 September 2017
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	[http://www.jstacs.de/downloads/jstacs_citation.bib BibTeX entry]		[http://www.jstacs.de/downloads/jstacs_citation.bib BibTeX entry]

			== JstacsFX ==
			JstacsFX is a library for building applications with graphical user interface based on Jstacs classes and using JavaFX.
			The current release of JstacsFX is available from [[Downloads \| here]] and an [http://www.jstacs.de/api-fx/index.html API documentation] is available.

			Example applications using JstacsFX for their graphical user interface are [[InMoDe]] and [[AnnoTALE]].

	== Applications ==		== Applications ==
	Applications currently using Jstacs:		Applications currently using Jstacs:

Grau: /* Applications */

2017-09-08T15:32:38Z

Applications

← Older revision		Revision as of 15:32, 8 September 2017
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	* [[GeMoMa]]		* [[GeMoMa]]
	* [[AnnoTALE]]		* [[AnnoTALE]]
			* [[InMoDe]]

	== Bug reports & Feature requests ==		== Bug reports & Feature requests ==

← Older revision		Revision as of 07:56, 13 June 2018
Line 64:		Line 64:

	== Latest Papers ==		== Latest Papers ==
			The paper '''''[[GeMoMa \| Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi]]''''' has been published in [https://link.springer.com/article/10.1186%2Fs12859-018-2203-5 BMC Bioinformatics].

	The paper '''''[[InMoDe \| InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites]]''''' has been published in [https://academic.oup.com/bioinformatics/article/33/4/580/2666342/InMoDe-tools-for-learning-and-visualizing-intra Bioinformatics].		The paper '''''[[InMoDe \| InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites]]''''' has been published in [https://academic.oup.com/bioinformatics/article/33/4/580/2666342/InMoDe-tools-for-learning-and-visualizing-intra Bioinformatics].

	The paper '''''[[AnnoTALE \| AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences]]''''' has been published in [http://www.nature.com/articles/srep21077 Scientific Reports].		The paper '''''[[AnnoTALE \| AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences]]''''' has been published in [http://www.nature.com/articles/srep21077 Scientific Reports].

	The paper '''''[[GeMoMa \| Using intron position conservation for homology-based gene predictions]]''''' has been published in [https://nar.oxfordjournals.org/content/early/2016/02/17/nar.gkw092 Nucleic Acids Research].

	The paper '''''[[PMMdeNovo \| Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data ]]''''' has been published in [http://www.biomedcentral.com/1471-2105/16/375 BMC Bioinformatics].		The paper '''''[[PMMdeNovo \| Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data ]]''''' has been published in [http://www.biomedcentral.com/1471-2105/16/375 BMC Bioinformatics].