GATE is a model-based, open source tool for chromatin states prediction based on time-course Epigenetic marks data.

Download and Installation

GATE is available for both Windows (32- and 64-bit) and Linux (64-bit) platforms, source file is also available to build with specific needs:

• GATE Package for 32-bit Windows
• GATE Package for 64-bit Linux (built under Ubuntu)
• GATE Package for 64-bit Windows
• Source code for FMM-HMM.dll/FMM-HMM.so

The package contains four files.

1. "FMM-HMM-functions.R": the main functions file, which contains three major functions: (1) Inputdata--To preprocess and change the data into readable format for FMM.HMM.program;  (2) FMM.HMM.program--main function for classification of chromatin states based on input epigenetic data; (3) grouping.clusters--To further group the clusters with information of parameters inferred in the model; (4) colorBED--To draw colorful BED file with clustering and hidden states information.
2. "FMM-HMM.dll"(windows)/"FMM-HMM.so"(Linux): dynamic library for the core part of the algorithm.
3. "Data.txt": a sample dataset for testing purposes ( See input data format ).
4. "Example.R": an example for how to use the algorithm.

To install the package:

1. Download the latest version of R for your platform from http://cran.r-project.org/.
2. Download the package for your platform and extract code files from the package file to a new folder.

Last updated on 07/01/2013 by Pengfei Yu