Software: rDiff
Description: Detection of differential Isoform expression
Authors: Philipp Drewe, Regina Bohnert, Oliver Stegle, Gunnar Raetsch et al.
URL: http://bioweb.me/rdiff

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  rDiff version 0.3
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DESCRIPTION
rDiff is a programme to determine abundances of multiple transcripts
per gene locus from RNA-Seq measurements. It can simultaneously
estimate the effect of biases introduced by experimental settings. 

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


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.

GALAXY
rDiff can be used as a web service embedded in a Galaxy instance
(cf. http://galaxy.raetschlab.org/root?tool_id=rdiffweb_1).
The Galaxy tool configuration file of rDiff is located in the
subdirectory galaxy along with XML file for loading example data and
instructions (rdiff_web.xml and rdiff_web_instructions.xml,
respectively). Please adapt the paths to the respective tools in
command section of the XML files as indicated.
The subdirectory test_data contains all data for running a functional
test in Galaxy (e.g. with sh run_functional_test.sh -id rdiffweb). You
may need to move these test files into the Galaxy test-data directory.

DOCUMENTATION
More information is available in doc/rdiff_web_instructions.txt and
doc/rdiff_web.txt. Examples for running rDiff can be found in
examples/./run_example.sh.
You can also find information on rDiff on
http://fml.mpg.de/raetsch/suppl/rdiff.
 
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, Andŕe Kahles, 
Regina Bohnert, Andreas Wachter, Karsten Borgwardt, Gunnar Raetsch,
Accurate Detection of Differential RNA Processing, NAR, 2013