MeDeMo - Revision history

Grau: /* Methylation Sensitivity */

2020-04-28T21:55:44Z

Methylation Sensitivity

← Older revision		Revision as of 21:55, 28 April 2020
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	<td>Predictions (The file containing the predictions from the training run)</td>		<td>Predictions (The file containing the predictions from the training run)</td>
	<td style="width:100px;">FILE</td>		<td style="width:100px;">FILE</td>
			</tr>
			<tr style="vertical-align:top">
			<td><font color="green">s</font></td>
			<td>Sequence column (The column of the predictions file containing the sequences in adjusted strand orientation, default = 8)</td>
			<td style="width:100px;">INT</td>
	</tr>		</tr>
	<tr style="vertical-align:top">		<tr style="vertical-align:top">

Grau: /* Download */

2020-03-23T23:00:08Z

Download

← Older revision		Revision as of 23:00, 23 March 2020
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	Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.		Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.

	~~Examples~~ data (also used for the code examples below) is [http://www.jstacs.de/downloads/MeDeMo-examples.~~tgz~~ available for download].		Example data (also used for the code examples below) are [http://www.jstacs.de/downloads/MeDeMo-examples.zip available for download].

	== Tools ==		== Tools ==

Grau: /* Download */

2020-03-21T13:16:22Z

Download

← Older revision		Revision as of 13:16, 21 March 2020
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	** [http://www.jstacs.de/downloads/MeDeMoGUI-1.0.jar JAR file] (requires installed Java >= 1.8 and JavaFX)		** [http://www.jstacs.de/downloads/MeDeMoGUI-1.0.jar JAR file] (requires installed Java >= 1.8 and JavaFX)
	** [http://www.jstacs.de/downloads/MeDeMo-1.0.zip Windows ZIP]: within the ZIP archive, you find the JAR and a custom Java runtime environment; to run MeDeMo, just double-click run.bat		** [http://www.jstacs.de/downloads/MeDeMo-1.0.zip Windows ZIP]: within the ZIP archive, you find the JAR and a custom Java runtime environment; to run MeDeMo, just double-click run.bat
	** [http://www.jstacs.de/downloads/MeDeMo-1.0.app.zip Mac App]: within the ZIP archive, you find a Mac-App, which you can copy anywhere you like (e.g., your /Applications folder) and run the app by double-clicking it; depending on your security settings, it might be necessary to use Right-click -> Open when opening MeDeMo for the first time and explicitly allow it to run; it might also be necessary to disable App (Right-click -> GetInfo -> Prevent App Nap)		** [http://www.jstacs.de/downloads/MeDeMo-1.0.app.zip Mac App]: within the ZIP archive, you find a Mac-App, which you can copy anywhere you like (e.g., your /Applications folder) and run the app by double-clicking it; depending on your security settings, it might be necessary to use Right-click -> Open when opening MeDeMo for the first time and explicitly allow it to run; it might also be necessary to disable "App Nap" (Right-click -> GetInfo -> Prevent App Nap)

	Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.		Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.

Grau: /* Download */

2020-03-21T11:21:14Z

Download

← Older revision		Revision as of 11:21, 21 March 2020
Line 11:		Line 11:
	** [http://www.jstacs.de/downloads/MeDeMoGUI-1.0.jar JAR file] (requires installed Java >= 1.8 and JavaFX)		** [http://www.jstacs.de/downloads/MeDeMoGUI-1.0.jar JAR file] (requires installed Java >= 1.8 and JavaFX)
	** [http://www.jstacs.de/downloads/MeDeMo-1.0.zip Windows ZIP]: within the ZIP archive, you find the JAR and a custom Java runtime environment; to run MeDeMo, just double-click run.bat		** [http://www.jstacs.de/downloads/MeDeMo-1.0.zip Windows ZIP]: within the ZIP archive, you find the JAR and a custom Java runtime environment; to run MeDeMo, just double-click run.bat
	** [http://www.jstacs.de/downloads/MeDeMo-1.0.~~dmg~~ Mac ~~DMG~~]: ~~Mac disk image; on~~ the ~~mounted image~~, you find a Mac-App, which you can copy anywhere you like (e.g., your /Applications folder) and run the app by double-clicking it		** [http://www.jstacs.de/downloads/MeDeMo-1.0.app.zip Mac App]: within the ZIP archive, you find a Mac-App, which you can copy anywhere you like (e.g., your /Applications folder) and run the app by double-clicking it; depending on your security settings, it might be necessary to use Right-click -> Open when opening MeDeMo for the first time and explicitly allow it to run; it might also be necessary to disable App (Right-click -> GetInfo -> Prevent App Nap)

	Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.		Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.

Grau: /* Download */

2020-03-21T00:29:14Z

Download

← Older revision		Revision as of 00:29, 21 March 2020
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	MeDeMo is available as		MeDeMo is available as
	* [http://www.jstacs.de/downloads/MeDeMo-1.0.jar command line interface] version and		* [http://www.jstacs.de/downloads/MeDeMo-1.0.jar command line interface] version and
	* graphical user interface version: [http://www.jstacs.de/downloads/MeDeMoGUI-1.0.jar JAR file] (requires Java >= 1.8 and JavaFX), [http://www.jstacs.de/downloads/~~MeDeMoGUI~~-1.0.~~exe~~ Windows ~~installer~~], [http://www.jstacs.de/downloads/~~MeDeMoGUI~~-1.0.dmg Mac DMG].		* graphical user interface version:
			** [http://www.jstacs.de/downloads/MeDeMoGUI-1.0.jar JAR file] (requires installed Java >= 1.8 and JavaFX)
			** [http://www.jstacs.de/downloads/MeDeMo-1.0.zip Windows ZIP]: within the ZIP archive, you find the JAR and a custom Java runtime environment; to run MeDeMo, just double-click run.bat
			** [http://www.jstacs.de/downloads/MeDeMo-1.0.dmg Mac DMG]: Mac disk image; on the mounted image, you find a Mac-App, which you can copy anywhere you like (e.g., your /Applications folder) and run the app by double-clicking it

	Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.		Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.

Grau: /* Download */

2020-03-19T13:15:40Z

Download

← Older revision		Revision as of 13:15, 19 March 2020
Line 12:		Line 12:
	Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.		Source code is available from the [https://github.com/Jstacs/Jstacs Jstacs github page] in package <code>projects.methyl</code>.

			Examples data (also used for the code examples below) is [http://www.jstacs.de/downloads/MeDeMo-examples.tgz available for download].

	== Tools ==		== Tools ==

Grau: /* Methylation Sensitivity */

2020-03-19T13:14:29Z

Methylation Sensitivity

← Older revision		Revision as of 13:14, 19 March 2020
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	'''Example:'''		'''Example:'''

	java -jar MeDeMo-1.0.jar msens		java -jar MeDeMo-1.0.jar msens m=2train/Motif_1/SlimDimont_1.xml p=2train/Motif_1/Predictions_for_motif_1.tsv outdir=5msens

Grau: /* Quick Prediction Tool */

2020-03-19T13:14:07Z

Quick Prediction Tool

← Older revision		Revision as of 13:14, 19 March 2020
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	'''Example:'''		'''Example:'''

	java -jar MeDeMo-1.0.jar quickpred		java -jar MeDeMo-1.0.jar quickpred d=2train/Motif_1/SlimDimont_1.xml s=0data/genomes/HepG2_converted_genome.unmasked.fa.gz sl=1e-5 outdir=6predict


	=== Methylation Sensitivity ===		=== Methylation Sensitivity ===

Grau: /* Motif scores */

2020-03-19T13:13:41Z

Motif scores

← Older revision		Revision as of 13:13, 19 March 2020
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	'''Example:'''		'''Example:'''

	java -jar MeDeMo-1.0.jar motif		java -jar MeDeMo-1.0.jar motif d=2train/Motif_1/SlimDimont_1.xml g=0data/genomes/HepG2_converted_genome.unmasked.fa.gz f=0data/genomes/HepG2_converted_genome.unmasked.fa.fai outdir=7scores b=50


	=== Quick Prediction Tool ===		=== Quick Prediction Tool ===

Grau: /* Evaluate Scoring */

2020-03-19T13:10:17Z

Evaluate Scoring

← Older revision		Revision as of 13:10, 19 March 2020
Line 362:		Line 362:
	'''Example:'''		'''Example:'''

	java -jar MeDeMo-1.0.jar eval		java -jar MeDeMo-1.0.jar eval p=3score/NRF1_GM12878/Predictions.tsv n=3score/negatives/Predictions.tsv c=true outdir=4eval


	=== Motif scores ===		=== Motif scores ===