Mercurial > repos > vladimir-daric > ebio_deseq


This program uses the `DESeq`_ R library to realize a differential analysis on feature count data from RNA-Seq experiments.
As input you have to provide a genomic features count date, such as provided by `HTSeq-count`_.
The script performs a normalisation of data and then the differential analysis (negative binomial test).
Several plots are produced.


The wrapper program (DESeq_diff_ann_wrapper.py) and R library GetOptions.R are 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.

Authors :
Vladimir Daric (eBio), Rachel Legendre (eBio), Coline Billerey (eBio), Alban Ott (IGM), Claire Wallon (eBio)


Licenses:

If **DESeq** is used to obtain results for scientific publications it should be cited as [1].
References:
[1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`.

Contact:
    ebio@igmors.u-psud.fr

.. _DESeq: http://bioconductor.org/packages/release/bioc/html/DESeq.html
.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/count.html
.. _eBio: http://ebio.u-psud.fr/
author	vladimir-daric
date	Fri, 25 Apr 2014 05:05:39 -0400
parents
children	a39532e4b01b