Mercurial > repos > vipints > rdiff

view rDiff/README @ 3:29a698dc5c7e default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Merge multiple heads.
author Dave Bouvier <dave@bx.psu.edu>
date Mon, 27 Jan 2014 14:15:36 -0500
parents 0f80a5141704
children
line wrap: on
line source

---------------------
  rDiff version 0.3
---------------------
http://bioweb.me/rdiff

DESCRIPTION
-----------
rDiff performs differential expression testing and 
creates a list of gene names with corresponding 
p-values.

REQUIREMENTS
------------
- Octave/Matlab >=3.4
- Python >=2.6.5 and Scipy >=0.7.1
- SAMTools >= 0.1.7

GETTING STARTED
---------------
To install rDiff and the required software please 
follow the instructions in INSTALL in this directory.

CONTENTS
--------
All relevant scripts for rDiff are located in the 
subdirectory src. rdiff.sh is the main script to 
start rDiff.

    ./bin
    Contains rdiff_config.sh file which is used for the configuration.
    According to your platform, the default file will be changed.

    ./galaxy
    Galaxy tool configuration files

    ./tools
    A python based GFF parsing program. Also contains small utils 
    programs.
            
    ./examples
    This sub-directory contains all data for running a functional 
    tests.

    ./mex 
    matlab executable files.

LICENSE
-------
rDiff is licensed under the GPL version 3 or any later version
(cf. LICENSE).

CITE US
-------
If you use rDiff in your research you are kindly asked to cite 
the following publication:

Philipp Drewe, Oliver Stegle, Lisa Hartmann, AndrĖe Kahles, 
Regina Bohnert, Andreas Wachter, Karsten Borgwardt, Gunnar Raetsch,
Accurate Detection of Differential RNA Processing, NAR, 2013

COPYRIGHT
---------
Copyright (C) 
        2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany
        2012-2013 Memorial Sloan-Kettering Cancer Center, New York City, USA 

CONTACT
-------
vipin@cbio.mskcc.org