Difference between revisions of "About GenPlay"

Revision as of 17:23, 23 May 2011

Introduction

GenPlay is an analyzer and browser for high-throughput data that is being developed by the Stem Cell Genomic Unit of the Einstein Pluripotent Stem Cell Center at the Albert Einstein College of Medicine of Yeshiva University in New York City.

Abstract

Rapidly decreasing sequencing cost due to the emergence and improvement of massively-parallel sequencing technologies has resulted in dramatic increase in the quantity of data that need to be analyzed. Therefore, software tools to process, visualize, analyze and integrate data produced on multiple platforms and using multiple methods are needed.

GenPlay is an extremely fast, easy to use and stable tool for rapid analysis and data processing that is being developed at Albert Einstein College of Medicine. Genplay, which is written in Java and runs on all major operating systems, can display data obtained either with micro-array based or sequencing based platforms. It displays tracks adapted to summarize gene structure, gene expression; repeat families, CPG islands, etc. and can also display custom tracks to show the results of RNA-seq, Chip-Seq or TimEX-seq analysis, for example.

GenPlay also offers a library of operations to process raw data (normalization, binning, smoothing) and to generate statistics (minimum, maximum, standard deviation, correlation etc). The tools provided include Gaussian filter, peak finders, signal saturation, island finders. It also has graphical features like scatter plots and bar charts to depict repartition and distances between genes.

The browser is currently being tested and used for in-house studies. The library of operations is growing based on the emerging needs. Contributions to the development of the software are welcome.

Source Code

The source code of GenPlay are available from the SVN repository at https://genplay.einstein.yu.edu/svn/GenPlay You can check out the latest source code with a SVN client with the following command:

svn co https://genplay.einstein.yu.edu/svn/GenPlay

Cite GenPlay

If you like GenPlay and use it for your research, please help us by citing our publication in Bioinformatics:

Bioinformatics. 2011 May 19
GenPlay, a multi-purpose genome analyzer and browser.
Lajugie J, Bouhassira E.
Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

PMID: 21596789

You can also link to GenPlay.net from your website to increase our visibility.

Thanks for supporting us!

Credit

GenPlay is being developed by Eric Bouhassira, Nicolas Fourel and Julien Lajugie
GenPlay is funded in part by NYSTEM

License

GenPlay, Einstein Genome Analyzer Copyright (C) 2009, 2011 Albert Einstein College of Medicine

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

The program "GenPlay" written by Julien Lajugie is available at http://genplay.einstein.yu.edu