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1 ---------------------
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2 rDiff version 0.3
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3 ---------------------
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4 http://bioweb.me/rdiff
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5
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6 DESCRIPTION
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7 -----------
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8 rDiff performs differential expression testing and
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9 creates a list of gene names with corresponding
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10 p-values.
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11
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12 REQUIREMENTS
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13 ------------
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14 - Octave/Matlab >=3.4
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15 - Python >=2.6.5 and Scipy >=0.7.1
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16 - SAMTools >= 0.1.7
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17
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18 GETTING STARTED
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19 ---------------
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20 To install rDiff and the required software please
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21 follow the instructions in INSTALL in this directory.
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22
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23 CONTENTS
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24 --------
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25 All relevant scripts for rDiff are located in the
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26 subdirectory src. rdiff.sh is the main script to
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27 start rDiff.
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28
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29 ./bin
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30 Contains rdiff_config.sh file which is used for the configuration.
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31 According to your platform, the default file will be changed.
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32
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33 ./galaxy
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34 Galaxy tool configuration files
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35
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36 ./tools
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37 A python based GFF parsing program. Also contains small utils
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38 programs.
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39
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40 ./examples
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41 This sub-directory contains all data for running a functional
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42 tests.
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43
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44 ./mex
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45 matlab executable files.
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46
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47 LICENSE
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48 -------
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49 rDiff is licensed under the GPL version 3 or any later version
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50 (cf. LICENSE).
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51
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52 CITE US
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53 -------
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54 If you use rDiff in your research you are kindly asked to cite
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55 the following publication:
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56
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57 Philipp Drewe, Oliver Stegle, Lisa Hartmann, AndrĖe Kahles,
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58 Regina Bohnert, Andreas Wachter, Karsten Borgwardt, Gunnar Raetsch,
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59 Accurate Detection of Differential RNA Processing, NAR, 2013
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60
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61 COPYRIGHT
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62 ---------
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63 Copyright (C)
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64 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany
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65 2012-2013 Memorial Sloan-Kettering Cancer Center, New York City, USA
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66
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67 CONTACT
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68 -------
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69 vipin@cbio.mskcc.org
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