From GersteinInfo

Contents 1 Transcription and Binding Analysis Tool (TBAT) 1.1 Documentation 1.1.1 Users Guide 1.1.2 Javadocs 1.1.3 UML 1.2 Get the program 1.3 Source Code 1.4 AnnotationLibrary Java Library 1.5 Acknowledgement of external libraries

Transcription and Binding Analysis Tool (TBAT)

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.

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 Java website.

Documentation

Users Guide

Users Guide (Google Doc)

Javadocs

AnnotationLibrary

TBAT-analyze

TBAT-compare

UML

Class Diagrams

Activity Diagrams

Get the program

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

TBAT-analyze

TBAT-compare

Source Code

TBAT is an open-source tool distributed under the XXX license. All source code is distributed as compressed JAR files.

AnnotationLibrary

TBAT-analyze

TBAT-compare

AnnotationLibrary Java Library

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.

Annotation Library

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.

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

Broad IGV BigFile

Apache Commons Math

Apache Commons CLI

Google Guava

graphs4j