https://github.com/ratschlab/RiboDiff

RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data
https://github.com/ratschlab/RiboDiff

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RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data

• Host: GitHub
• URL: https://github.com/ratschlab/RiboDiff
• Owner: ratschlab
• License: gpl-3.0
• Created: 2015-03-10T14:55:02.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2016-10-03T18:29:11.000Z (about 8 years ago)
• Last Synced: 2024-06-30T14:52:37.032Z (4 months ago)
• Language: Python
• Size: 2.9 MB
• Stars: 21
• Watchers: 9
• Forks: 16
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: COPYING

Awesome Lists containing this project

• awesome-riboseq - Code

README

        
SOFTWARE: RiboDiff

----------

###VERSION

0.2.1

###Authors

Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin Sreedharan, David Kuo and Gunnar Raetsch.

###DESCRIPTION

RiboDiff is a statistical tool to detect the protein translation 

efficiency change from ribosome footprint profiling data and RNA-Seq

data under two different experimental conditions.

###URL

http://bioweb.me/ribodiff

###REQUIREMENTS

* Python2 >= 2.6.6 (Python3 is not supported yet.)

* Numpy >= 1.8.0

* Scipy >= 0.13.3

* Matplotlib >= 1.3.0 

* Statsmodels >= 0.5.0

These requirements can either be installed individually or as a Python distribution

that includes all the required packages. Please find more details at

http://www.scipy.org/install.html

###INSTALLATION

To install RiboDiff, please refer to INSTALL file in this directory.

###CONTENTS

All relevant scripts for RiboDiff are located in the subdirectory src. 

* src - main codebase for RiboDiff;

* tests - dataset and script for functional test;

* test-data - test dataset for Galaxy system;

        (move to your galaxy_root_folder/test-data/)

        You may need to move the test files into your test-data directory so galaxy can find them. 

        If you want to run the functional tests example as: 

        sh run_functional_tests.sh -id ribodiff

* tools - util functions for simulating negative binomial count data.

* scripts - TE.py - the main script to start RiboDiff.

###GALAXY

https://galaxy.cbio.mskcc.org/tool_runner?tool_id=ribodiff

###DOCUMENTATION

To use RiboDiff, please refer to the instructions in MANUAL in this directory.

###LICENSE

RiboDiff is licensed under the GPL version 3 or any later version

(cf. LICENSE).

###CITE US

If you use RiboDiff in your research you are kindly asked to cite the

following publication:

Zhong Y, Karaletsos T, Drewe P, et al. RiboDiff: Detecting Changes of Translation 

Efficiency from Ribosome Footprints. bioRxiv. doi: 10.1101/017111.