CAPE

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=Analysis of Polymerase and Expression (APE)=
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[[File:CAPE.png]]
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APE Is designed with two primary goals in mind.  The first is to associate transcription factor binding site data from next-generation sequencing experiments such as ChIP-Seq with a set of genomic features such as transcription start sites, transcription end sites, etc.  The second aim is to classify transcripts in a genome based on levels of transcription factor binding at the promoter vs the expression level of the transcript.  APE is designed to work with many of the formats employed by large consortia such as NHGRI’s ENCODE and modENCODE consortia.
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=Coupled Analysis of Polymerase and Expression (CAPE)=
 +
CAPE Is designed with two primary goals in mind.  The first is to associate transcription factor binding site data from next-generation sequencing experiments such as ChIP-Seq with a set of genomic features such as transcription start sites, transcription end sites, etc.  The second aim is to classify transcripts in a genome based on levels of transcription factor binding at the promoter vs the expression level of the transcript.  CAPE is designed to work with many of the formats employed by large consortia such as NHGRI’s ENCODE and modENCODE consortia.
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APE 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://java.sun.com 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].
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==Documentation==
 
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===Users Guide===
 
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[https://docs.google.com/document/d/1k8RMymsbl2DikRHkOwj5tNnSA6y_9UReYjLWCFD4gRo/edit Users Guide (Google Doc)]
 
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===Javadocs===
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==Get the Program==
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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/APE/docs/javadoc/AnnotationLibrary/ AnnotationLibrary]
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[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-analyze.jar CAPE-analyze]
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[http://archive.gersteinlab.org/proj/APE/docs/javadoc/APE-analyze/ APE-analyze]
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[http://archive.gersteinlab.org/proj/CAPE/bin/CAPE-compare.jar CAPE-compare]
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[http://archive.gersteinlab.org/proj/APE/docs/javadoc/APE-compare/ APE-compare]
 
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===UML===
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==AnnotationLibrary Java Library==
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[[TBAT Class Diagrams|Class Diagrams]]
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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.
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[[TBAT Activity Diagrams|Activity Diagrams]]
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[http://archive.gersteinlab.org/proj/CAPE/lib/AnnotationLibrary.jar AnnotationLibrary]
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==Get the program==
+
==Documentation==
-
APE programs are distributed as executable JAR files. Please see the Users Guide for more information.
+
===Users Guide===
 +
[https://docs.google.com/document/d/1k8RMymsbl2DikRHkOwj5tNnSA6y_9UReYjLWCFD4gRo/edit CAPE Users Guide (Google Doc)]
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[http://archive.gersteinlab.org/proj/APE/bin/APE-analyze.jar APE-analyze]
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[http://archive.gersteinlab.org/proj/CAPE/docs/misc/CAPE_Users_Guide.pdf CAPE Users Guide (PDF)]
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[http://archive.gersteinlab.org/proj/APE/bin/APE-compare.jar APE-compare]
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===Use Cases===
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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.
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[http://archive.gersteinlab.org/proj/CAPE/usecases/CAPE_Use_Cases.pdf CAPE Use Cases]
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==Source Code==
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===Javadocs===
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APE is an open-source tool distributed under the XXX license. All source code is distributed as compressed JAR files.
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[http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/AnnotationLibrary/ AnnotationLibrary]
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[http://archive.gersteinlab.org/proj/APE/src/AnnotationLibrary-src.jar AnnotationLibrary]
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[http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/CAPE-analyze/ CAPE-analyze]
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[http://archive.gersteinlab.org/proj/APE/src/APE-analyze-src.jar APE-analyze]
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[http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/CAPE-compare/ CAPE-compare]
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[http://archive.gersteinlab.org/proj/APE/src/APE-compare-src.jar APE-compare]
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===UML===
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[[CAPE Activity Diagrams|Activity Diagrams]]
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==AnnotationLibrary Java Library==
+
[[CAPE Class Diagrams|Class Diagrams]]
-
APE 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/APE/lib/AnnotationLibrary.jar Annotation Library]
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==Source Code==
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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.
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==Acknowledgement of external libraries==
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[http://archive.gersteinlab.org/proj/CAPE/src/CAPEanalyze-src.jar CAPE-analyze]
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APE-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. APE-compare utilizes the Apache Commons CLI and charts4j external libraries. These libraries are included as part of the respective executable jar file in their original, unaltered forms.
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[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]
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For more information on each library, please see the following links:
 
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[http://http://code.google.com/p/bigwig/ Broad IGV BigFile]
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==Acknowledgement of External Libraries==
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[http://commons.apache.org/math/ Apache Commons Math]
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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.
 +
 
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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]
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 +
[http://commons.apache.org/math/ Apache Commons Math]
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 +
[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]
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[http://code.google.com/p/charts4j/ graphs4j]
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[http://cran.r-project.org/web/packages/VennDiagram/index.html VennDiagram]

Latest revision as of 16:58, 3 July 2012

File:CAPE.png

Contents

Coupled Analysis of Polymerase and Expression (CAPE)

CAPE Is designed with two primary goals in mind. The first is to associate transcription factor binding site data from next-generation sequencing experiments such as ChIP-Seq with a set of genomic features such as transcription start sites, transcription end sites, etc. The second aim is to classify transcripts in a genome based on levels of transcription factor binding at the promoter vs the expression level of the transcript. CAPE is designed to work with many of the formats employed by large consortia such as NHGRI’s ENCODE and modENCODE consortia.


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 Java website.


Get the Program

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

CAPE-analyze

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.

AnnotationLibrary


Documentation

Users Guide

CAPE Users Guide (Google Doc)

CAPE Users Guide (PDF)

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. If your browser is having trouble opening the pdf file, please right-click the link, select "Save Link As...", and view the saved file.

CAPE Use Cases

Javadocs

AnnotationLibrary

CAPE-analyze

CAPE-compare

UML

Activity Diagrams

Class Diagrams


Source Code

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.

CAPE-analyze

CAPE-compare


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.

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

Apache Commons CLI

Apache Commons Math

Broad IGV BigFile

Google Guava

VennDiagram

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