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== Introduction ==
GenPlay is an analyzer and browser for high-throughput data that is being developed by the Stem Cell Genomic Unit at the [http://genplay.net/home/default.asp Albert Einstein College of Medicine] of [http://www.yu.edu/ 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 GIT repository at https://github.com/JulienLajugie/GenPlay
You can check out the latest source code with a git client with the following command:
  git clone git://github.com/JulienLajugie/GenPlay.git

== Report Bugs ==
Please help us improve GenPlay by reporting bugs at https://github.com/JulienLajugie/GenPlay/issues

== Cite GenPlay ==
If you like GenPlay and use it for your research, please help us by citing our publication in  [http://bioinformatics.oxfordjournals.org/content/27/14/1889 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.

Thank you for your support!

== Credit ==
GenPlay is being developed by [mailto:julien.lajugie@gmail.com?Subject=Email%20from%20genplay.net Julien Lajugie], Nicolas Fourel and Eric Bouhassira.
<br>GenPlay was funded in part by [http://stemcell.ny.gov/ NYSTEM]

== License ==
GenPlay, Einstein Genome Analyzer
Copyright (C) 2009, 2013 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 
[mailto:julien.lajugie@gmail.com?Subject=Email%20from%20genplay.net Julien Lajugie]  is available at http://genplay.net
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