CAPE
From GersteinInfo
Contents |
Analysis of Polymerase and Expression (APE)
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.
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 Java website.
Documentation
Users Guide
Javadocs
UML
Get the program
APE programs are distributed as executable JAR files. Please see the Users Guide for more information.
Source Code
APE is an open-source tool distributed under the XXX license. All source code is distributed as compressed JAR files.
AnnotationLibrary Java Library
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.
Acknowledgement of external libraries
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.
For more information on each library, please see the following links:
