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README : EXPRESS
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eXpress is a streaming DNA/RNA sequence quantification tool. It has initially 
been tested for RNA-Seq transcriptome quantification but can be used in any 
application where abundances of target sequences need to be estimated from short 
reads sequenced from them.

More details, installation instructions, and the manual can be found at 
http://bio.math.berkeley.edu/eXpress/

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I.   Authors:
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The methods and algorithms used in eXpress were developed by Adam Roberts and 
Lior Pachter. Adam Roberts designed and wrote eXpress. 

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II.  Requirements:
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eXpress is a standalone tool that requires gcc 4.0 or greater, and runs on Linux 
Macintosh OS X, and Windows.  

It depends on Boost (http://www.boost.org), 
BamTools (https://github.com/pezmaster31/bamtools),
ZLIB (http://zlib.net/),
and the Microsoft Visual C++ Runtime Library (Windows only) 
(http://www.microsoft.com/download/en/details.aspx?id=5555).


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III. Learn More (Installation, Manual, etc.):
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Installation steps, tutorial, manual, documentation, etc. are all available 
through the eXpress website:
http://bio.math.berkeley.edu/eXpress/

Join the user group and mailing list to stay informed of updates and announcements:
http://groups.google.com/group/express-users

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IV.  License:
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eXpress is distributed under the Artistic License 2.0.
Copyright (c) 2011-2013 Adam Roberts and Lior Pachter.

See included file LICENSE for details.

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V.   Acknowledgements:
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* Cole Trapnell, primary developer of Cufflinks
* Derek Barnett, author of the BamTools API

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VI.  References:
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Roberts A (2013). Thesis: Ambiguous fragment assignment for high-throughput
sequencing experiments. EECS Department, University of California, Berkeley.

Roberts A and Pachter L (2012). Streaming fragment assignment for real-time
analysis of sequencing experiments. Nature Methods.

eXpress builds upon many ideas, including some proposed in the following papers:

Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, 
Salzberg SL, Wold B and Pachter L (2010). Transcript assembly and quantification 
by RNA-Seq reveals unannotated transcripts and isoform switching during cell 
differentiation. Nature Biotechnology.

Cappé O and Moulines E (2009).  On-line expectation–maximization algorithm for 
latent data models. Journal of the Royal Statistical Society.

Pachter, L (2011). Models for transcript quantification from RNA-Seq. 
arXiv:1104.3889v2. 

Roberts A, Trapnell C, Donaghey J, Rinn JL and Pachter L (2011). Improving 
RNA-Seq expression estimates by correcting for fragment bias. Genome Biology. 

Li B and Dewey C (2011). RSEM: accurate transcript quantification from RNA-Seq 
data with or without a reference genome. BMC Bioinformatics. 

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VII. CONTACT:
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Please send all questions, comments, and suggestions to [email protected].