Mercurial > repos > vipints > deseq_hts

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A Galaxy wrapper for DEXSeq version 1.6.0
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DEXSeq is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs.
DEXSeq: http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html

Requirements:
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    Python, HTSeq package :- Preprocessing of sequencing reads and GFF files
    R, Bio-conductor package :- Required for DEXSeq
    SAMTOOLS :- Sequencing read processing

Contents:
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./bin
    Contains a config file for running DEXSeq in different settings, setup_dexseq-hts.sh
    will help to create the config file according to your local work station.

./setup_dexseq-hts.sh
    Setup script, which helps to set the right path to the config file present in the bin
    folder.

./README
    Basic information about the wrapper

./galaxy
    Galaxy tool configuration file can be found here.

./src
    All relevant scripts for DEXSeq execution, Please follow the shell script to
    understand the details.

Licenses:
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    If DEXSeq is used to obtain results for scientific publications it should be cited as [1].

    This wrapper 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.

    Copyright(C) 2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.

References
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    [1] Simon Anders and Alejandro Reyes and Wolfgang Huber (2012): Detecting differential usage of exons from RNA-seq data.

Contact:
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    support [at] oqtans.org
author	vipints <vipin@cbio.mskcc.org>
date	Tue, 08 Oct 2013 08:22:45 -0400
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