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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.

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.



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.



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






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.



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


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