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=Transcription and Binding Analysis Tool (TBAT)=
[[File:CAPE.png]]


TBAT 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.  This tool is designed to work with many of the formats employed by large consortia such as NHGRI’s ENCODE and modENCODE consortia.
=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.


TBAT 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].


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


===Javadocs===
==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]


[http://archive.gersteinlab.org/proj/TBAT/docs/javadoc/AnnotationLibrary/ AnnotationLibrary]


[http://archive.gersteinlab.org/proj/TBAT/docs/javadoc/TBAT-analyze/ TBAT-analyze]
==AnnotationLibrary Java Library==


[http://archive.gersteinlab.org/proj/TBAT/docs/javadoc/TBAT-compare/ TBAT-compare]
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.


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


[[TBAT Class Diagrams|Class Diagrams]]


[[TBAT Activity Diagrams|Activity Diagrams]]
==Documentation==
===Users Guide===
[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)]


==Get the program==
===Use Cases===
TBAT programs are distributed as executable JAR files. Please see the Users Guide for more information.
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/TBAT/bin/TBAT-analyze.jar TBAT-analyze]
[http://archive.gersteinlab.org/proj/CAPE/usecases/CAPE_Use_Cases.pdf CAPE Use Cases]


[http://archive.gersteinlab.org/proj/TBAT/bin/TBAT-compare.jar TBAT-compare]
===Javadocs===


[http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/AnnotationLibrary/ AnnotationLibrary]


==Source Code==
[http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/CAPE-analyze/ CAPE-analyze]


TBAT is an open-source tool distributed under the XXX license. All source code is distributed as compressed JAR files.
[http://archive.gersteinlab.org/proj/CAPE/docs/javadoc/CAPE-compare/ CAPE-compare]


[http://archive.gersteinlab.org/proj/TBAT/src/AnnotationLibrary-src.jar AnnotationLibrary]
===UML===


[http://archive.gersteinlab.org/proj/TBAT/src/TBAT-analyze-src.jar TBAT-analyze]
[[CAPE Activity Diagrams|Activity Diagrams]]


[http://archive.gersteinlab.org/proj/TBAT/src/TBAT-compare-src.jar TBAT-compare]
[[CAPE Class Diagrams|Class Diagrams]]




==AnnotationLibrary Java Library==
==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.


TBAT 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/src/CAPEanalyze-src.jar CAPE-analyze]


[http://archive.gersteinlab.org/proj/TBAT/lib/AnnotationLibrary.jar Annotation Library]
[http://archive.gersteinlab.org/proj/CAPE/src/CAPEcompare-src.jar CAPE-compare]




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


TBAT-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. TBAT-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.
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://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://code.google.com/p/charts4j/ graphs4j]
[http://cran.r-project.org/web/packages/VennDiagram/index.html VennDiagram]

Latest revision as of 16:58, 3 July 2012

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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