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version 0.3 uploaded
author vipints
date Thu, 14 Feb 2013 23:38:36 -0500
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1 ---------------------
2 rDiff version 0.3
3 ---------------------
4 http://bioweb.me/rdiff
5
6 DESCRIPTION
7 -----------
8 rDiff performs differential expression testing and
9 creates a list of gene names with corresponding
10 p-values.
11
12 REQUIREMENTS
13 ------------
14 - Octave/Matlab >=3.4
15 - Python >=2.6.5 and Scipy >=0.7.1
16 - SAMTools >= 0.1.7
17
18 GETTING STARTED
19 ---------------
20 To install rDiff and the required software please
21 follow the instructions in INSTALL in this directory.
22
23 CONTENTS
24 --------
25 All relevant scripts for rDiff are located in the
26 subdirectory src. rdiff.sh is the main script to
27 start rDiff.
28
29 ./bin
30 Contains rdiff_config.sh file which is used for the configuration.
31 According to your platform, the default file will be changed.
32
33 ./galaxy
34 Galaxy tool configuration files
35
36 ./tools
37 A python based GFF parsing program. Also contains small utils
38 programs.
39
40 ./examples
41 This sub-directory contains all data for running a functional
42 tests.
43
44 ./mex
45 matlab executable files.
46
47 LICENSE
48 -------
49 rDiff is licensed under the GPL version 3 or any later version
50 (cf. LICENSE).
51
52 CITE US
53 -------
54 If you use rDiff in your research you are kindly asked to cite
55 the following publication:
56
57 Philipp Drewe, Oliver Stegle, Lisa Hartmann, AndrĖe Kahles,
58 Regina Bohnert, Andreas Wachter, Karsten Borgwardt, Gunnar Raetsch,
59 Accurate Detection of Differential RNA Processing, NAR, 2013
60
61 COPYRIGHT
62 ---------
63 Copyright (C)
64 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany
65 2012-2013 Memorial Sloan-Kettering Cancer Center, New York City, USA
66
67 CONTACT
68 -------
69 vipin@cbio.mskcc.org