Mercurial > repos > vipints > rdiff
comparison rDiff/README @ 0:0f80a5141704
version 0.3 uploaded
| author | vipints |
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| date | Thu, 14 Feb 2013 23:38:36 -0500 |
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| -1:000000000000 | 0:0f80a5141704 |
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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, AndrĖe 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 |