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Tests for Differential RNA Isoform Expression
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Software: rDiff Description: Detection of differential Isoform expression Authors: Philipp Drewe, Regina Bohnert, Oliver Stegle, Gunnar Raetsch et al. URL: http://bioweb.me/rdiff --------------------- rDiff version 0.3 --------------------- 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