CAPE - Revision history

Public at 16:58, 3 July 2012

2012-07-03T16:58:14Z

← Older revision		Revision as of 16:58, 3 July 2012
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			[[File:CAPE.png]]

	=Coupled Analysis of Polymerase and Expression (CAPE)=		=Coupled Analysis of Polymerase and Expression (CAPE)=

Public at 06:03, 2 July 2012

2012-07-02T06:03:07Z

← Older revision		Revision as of 06:03, 2 July 2012
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	[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]


	==AnnotationLibrary Java Library==		==AnnotationLibrary Java Library==
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	[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]


	==Acknowledgement of External Libraries==		==Acknowledgement of External Libraries==

Public: /* Acknowledgement of external libraries */

2012-07-02T06:02:22Z

Acknowledgement of external libraries

← Older revision		Revision as of 06:02, 2 July 2012
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	[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]

	==Acknowledgement of ~~external libraries~~==		==Acknowledgement of External Libraries==

	CAPE-analyze makes use of the following external, publicly-available libraries: Google Guava, Apache Commons Math, Apache Commons CLI, and the Broad Institute’s IGV BigFile. CAPE-compare utilizes the Apache Commons CLI external library as well as the VennDiagram R package. The Java libraries are included as part of the respective executable jar file in their original, unaltered forms. VennDiagram can be downloaded from the link below or installed directly from R.		CAPE-analyze makes use of the following external, publicly-available libraries: Google Guava, Apache Commons Math, Apache Commons CLI, and the Broad Institute’s IGV BigFile. CAPE-compare utilizes the Apache Commons CLI external library as well as the VennDiagram R package. The Java libraries are included as part of the respective executable jar file in their original, unaltered forms. VennDiagram can be downloaded from the link below or installed directly from R.

Public: /* Get the program */

2012-07-02T06:02:05Z

Get the program

← Older revision		Revision as of 06:02, 2 July 2012
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	==Get the ~~program~~==		==Get the Program==
	CAPE programs are distributed as executable JAR files. Please see the Users Guide for more information.		CAPE programs are distributed as executable JAR files. Please see the Users Guide for more information.

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	[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]


	==AnnotationLibrary Java Library==		==AnnotationLibrary Java Library==

Public: /* Source Code */

2012-07-02T06:01:37Z

Source Code

← Older revision		Revision as of 06:01, 2 July 2012
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	==Source Code==		==Source Code==

	CAPE is open source software. All source code is distributed as compressed JAR files.		CAPE is open source software. All source code is distributed as compressed JAR files. AnnotationLibrary's source code can be obtained by decompressing the AnnotationLibrary.jar file downloaded above.

	[http://archive.gersteinlab.org/proj/CAPE/src/CAPEanalyze-src.jar CAPE-analyze]		[http://archive.gersteinlab.org/proj/CAPE/src/CAPEanalyze-src.jar CAPE-analyze]

	[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]


	==Acknowledgement of external libraries==		==Acknowledgement of external libraries==

Public: /* Acknowledgement of external libraries */

2012-07-02T06:00:19Z

Acknowledgement of external libraries

← Older revision		Revision as of 06:00, 2 July 2012
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	CAPE-analyze makes use of the following external, publicly-available libraries: Google Guava, Apache Commons Math, Apache Commons CLI, and the Broad Institute’s IGV BigFile. CAPE-compare utilizes the Apache Commons CLI external library as well as the VennDiagram R package. The Java libraries are included as part of the respective executable jar file in their original, unaltered forms. VennDiagram can be downloaded from the link below or installed directly from R.		CAPE-analyze makes use of the following external, publicly-available libraries: Google Guava, Apache Commons Math, Apache Commons CLI, and the Broad Institute’s IGV BigFile. CAPE-compare utilizes the Apache Commons CLI external library as well as the VennDiagram R package. The Java libraries are included as part of the respective executable jar file in their original, unaltered forms. VennDiagram can be downloaded from the link below or installed directly from R.

	For more information on each library, please see the following links:		For more information on each library, please see the following external links:

	[http://commons.apache.org/cli/ Apache Commons CLI]		[http://commons.apache.org/cli/ Apache Commons CLI]

Public: /* Use Cases */

2012-07-02T06:00:02Z

Use Cases

← Older revision		Revision as of 06:00, 2 July 2012
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	===Use Cases===		===Use Cases===
	The Use Cases document shows several sample workflows for CAPE. Example runs as well as links to sample data and output files are included in the document.		The Use Cases document shows several sample workflows for CAPE. Example runs as well as links to sample data and output files are included in the document. If your browser is having trouble opening the pdf file, please right-click the link, select "Save Link As...", and view the saved file.

	[http://archive.gersteinlab.org/proj/CAPE/usecases/CAPE_Use_Cases.pdf CAPE Use Cases]		[http://archive.gersteinlab.org/proj/CAPE/usecases/CAPE_Use_Cases.pdf CAPE Use Cases]

Public at 05:55, 2 July 2012

2012-07-02T05:55:21Z

← Older revision		Revision as of 05:55, 2 July 2012
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	CAPE is written in Java and requires Java version 1.6 or higher. The Java runtime environment (JRE) must be installed. If the JRE is not installed (i.e. typing “java –version” at the command line does not produce a version number or the version number is < 1.6), an updated version of the Java Runtime Environment can be downloaded from the [http://www.oracle.com/technetwork/java/index.html Java website].		CAPE is written in Java and requires Java version 1.6 or higher. The Java runtime environment (JRE) must be installed. If the JRE is not installed (i.e. typing “java –version” at the command line does not produce a version number or the version number is < 1.6), an updated version of the Java Runtime Environment can be downloaded from the [http://www.oracle.com/technetwork/java/index.html Java website].


			==Get the program==
			CAPE programs are distributed as executable JAR files. Please see the Users Guide for more information.

			[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-analyze.jar CAPE-analyze]

			[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]


			==AnnotationLibrary Java Library==

			CAPE makes use of the org.gersteinlab.annotation package, a series of classes and data structures written in Java. This library is already included in the JAR files for the above programs, but is also made available for the developer community as a separate compressed JAR file.

			[http://archive.gersteinlab.org/proj/CAPE/lib/AnnotationLibrary.jar AnnotationLibrary]


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	===Users Guide===		===Users Guide===
	[https://docs.google.com/document/d/1k8RMymsbl2DikRHkOwj5tNnSA6y_9UReYjLWCFD4gRo/edit CAPE Users Guide (Google Doc)]		[https://docs.google.com/document/d/1k8RMymsbl2DikRHkOwj5tNnSA6y_9UReYjLWCFD4gRo/edit CAPE Users Guide (Google Doc)]

			[http://archive.gersteinlab.org/proj/CAPE/docs/misc/CAPE_Users_Guide.pdf CAPE Users Guide (PDF)]

	===Use Cases===		===Use Cases===
			The Use Cases document shows several sample workflows for CAPE. Example runs as well as links to sample data and output files are included in the document.

	[http://archive.gersteinlab.org/proj/CAPE/usecases/CAPE_Use_Cases.pdf CAPE Use Cases]		[http://archive.gersteinlab.org/proj/CAPE/usecases/CAPE_Use_Cases.pdf CAPE Use Cases]

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	===UML===		===UML===

	~~[[CAPE Class Diagrams\|Class Diagrams]]~~

	[[CAPE Activity Diagrams\|Activity Diagrams]]		[[CAPE Activity Diagrams\|Activity Diagrams]]

			[[CAPE Class Diagrams\|Class Diagrams]]
	~~==Get the program==~~
	~~CAPE programs are distributed as executable JAR files. Please see the Users Guide for more information.~~

	[~~http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-analyze.jar~~ CAPE~~-analyze~~]

	~~[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare~~]


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	CAPE is open source software. All source code is distributed as compressed JAR files.		CAPE is open source software. All source code is distributed as compressed JAR files.

	~~[http://archive.gersteinlab.org/proj/CAPE/src/AnnotationLibrary-src.jar AnnotationLibrary]~~

	[http://archive.gersteinlab.org/proj/CAPE/src/CAPEanalyze-src.jar CAPE-analyze]		[http://archive.gersteinlab.org/proj/CAPE/src/CAPEanalyze-src.jar CAPE-analyze]

	[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]


	~~==AnnotationLibrary Java Library==~~

	CAPE makes use of the org.gersteinlab.annotation package, a series of classes and data structures written in Java. This library is already included in the JAR files for the above programs, but is also made available for the developer community as a separate JAR file.

	~~[http://archive.gersteinlab.org/proj/CAPE/lib/AnnotationLibrary.jar AnnotationLibrary]~~


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	For more information on each library, please see the following links:		For more information on each library, please see the following links:

	[http://~~http://code~~.~~google~~.~~com/p~~/~~bigwig~~/ ~~Broad IGV BigFile~~]		[http://commons.apache.org/cli/ Apache Commons CLI]

	[http://commons.apache.org/math/ Apache Commons Math]		[http://commons.apache.org/math/ Apache Commons Math]

	[http://~~commons~~.~~apache~~.~~org~~/~~cli~~/ ~~Apache Commons CLI~~]		[http://http://code.google.com/p/bigwig/ Broad IGV BigFile]

	[http://code.google.com/p/guava-libraries/ Google Guava]		[http://code.google.com/p/guava-libraries/ Google Guava]

	[http://cran.r-project.org/web/packages/VennDiagram/index.html VennDiagram]		[http://cran.r-project.org/web/packages/VennDiagram/index.html VennDiagram]

Public at 21:06, 28 June 2012

2012-06-28T21:06:20Z

← Older revision		Revision as of 21:06, 28 June 2012
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	CAPE is written in Java and requires Java version 1.6 or higher. The Java runtime environment (JRE) must be installed. If the JRE is not installed (i.e. typing “java –version” at the command line does not produce a version number or the version number is < 1.6), an updated version of the Java Runtime Environment can be downloaded from the [http://www.oracle.com/technetwork/java/index.html Java website].		CAPE is written in Java and requires Java version 1.6 or higher. The Java runtime environment (JRE) must be installed. If the JRE is not installed (i.e. typing “java –version” at the command line does not produce a version number or the version number is < 1.6), an updated version of the Java Runtime Environment can be downloaded from the [http://www.oracle.com/technetwork/java/index.html Java website].


	==Documentation==		==Documentation==
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	[[CAPE Activity Diagrams\|Activity Diagrams]]		[[CAPE Activity Diagrams\|Activity Diagrams]]


	==Get the program==		==Get the program==
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	[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]


	==Source Code==		==Source Code==
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	[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]


	==AnnotationLibrary Java Library==		==AnnotationLibrary Java Library==
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	[http://archive.gersteinlab.org/proj/CAPE/lib/AnnotationLibrary.jar AnnotationLibrary]		[http://archive.gersteinlab.org/proj/CAPE/lib/AnnotationLibrary.jar AnnotationLibrary]


	==Acknowledgement of external libraries==		==Acknowledgement of external libraries==

Public at 20:55, 28 June 2012

2012-06-28T20:55:11Z

← Older revision		Revision as of 20:55, 28 June 2012
Line 5:		Line 5:

	CAPE is written in Java and requires Java version 1.6 or higher. The Java runtime environment (JRE) must be installed. If the JRE is not installed (i.e. typing “java –version” at the command line does not produce a version number or the version number is < 1.6), an updated version of the Java Runtime Environment can be downloaded from the [http://www.oracle.com/technetwork/java/index.html Java website].		CAPE is written in Java and requires Java version 1.6 or higher. The Java runtime environment (JRE) must be installed. If the JRE is not installed (i.e. typing “java –version” at the command line does not produce a version number or the version number is < 1.6), an updated version of the Java Runtime Environment can be downloaded from the [http://www.oracle.com/technetwork/java/index.html Java website].


	==Documentation==		==Documentation==
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	[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]		[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]


	==Source Code==		==Source Code==