CAPE
From GersteinInfo
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| - | =Analysis of Polymerase and Expression ( | + | =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 [http://www.oracle.com/technetwork/java/index.html Java website]. | |
| Line 13: | Line 13: | ||
===Javadocs=== | ===Javadocs=== | ||
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/AnnotationLibrary/ AnnotationLibrary] |
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/APE-analyze/ APE-analyze] |
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/APE-compare/ APE-compare] |
===UML=== | ===UML=== | ||
| - | [[ | + | [[CAPE Class Diagrams|Class Diagrams]] |
| - | [[ | + | [[CAPE Activity Diagrams|Activity Diagrams]] |
==Get the program== | ==Get the program== | ||
| - | + | CAPE programs are distributed as executable JAR files. Please see the Users Guide for more information. | |
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/bin/APE-analyze.jar CAPE-analyze] |
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/bin/APE-compare.jar CAPE-compare] |
==Source Code== | ==Source Code== | ||
| - | + | CAPE is open source software. All source code is distributed as compressed JAR files. | |
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/src/AnnotationLibrary-src.jar AnnotationLibrary] |
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/src/APE-analyze-src.jar APE-analyze] |
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/CAPE/src/APE-compare-src.jar APE-compare] |
==AnnotationLibrary Java Library== | ==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/APE/lib/AnnotationLibrary.jar Annotation Library] | [http://archive.gersteinlab.org/proj/APE/lib/AnnotationLibrary.jar Annotation Library] | ||
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==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. | |
For more information on each library, please see the following links: | For more information on each library, please see the following links: | ||
| Line 66: | Line 66: | ||
[http://code.google.com/p/guava-libraries/ Google Guava] | [http://code.google.com/p/guava-libraries/ Google Guava] | ||
| - | [http:// | + | [http://cran.r-project.org/web/packages/VennDiagram/index.html VennDiagram] |
Revision as of 17:01, 26 June 2012
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.
Documentation
Users Guide
Javadocs
UML
Get the program
CAPE programs are distributed as executable JAR files. Please see the Users Guide for more information.
Source Code
CAPE is open source software. All source code is distributed as compressed JAR files.
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.
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 links:
