LBMC » NucleoMiner

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Readme / Documentation for `NucleoMiner2`

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`NucleoMiner2` offers Python API and R package allowing to perform 

quantitative analysis of nucleosomal epigenome. It is especially well 

suited for scripting to extract natural Single-Nucleosome Epi-

Polymorphisms (SNEP) from ChIP-Seq data.

License

=======

Copyright CNRS 2012-2013                                                 

- Florent CHUFFART                                                         

- Jean-Baptiste VEYRIERAS                                                  

- Gael YVERT                                                               

This software is a computer program which purpose is to perform quanti-

tative analysis of epigenetic marks at single nucleosome resolution.     

This software is governed by the CeCILL license under French law and     

abiding by the rules of distribution of free software.  You can  use,    

modify and/ or redistribute the software under the terms of the CeCILL   

license as circulated by CEA, CNRS and INRIA at the following URL        

"http://www.cecill.info".                                                

As a counterpart to the access to the source code and  rights to copy,   

modify and redistribute granted by the license, users are provided only  

with a limited warranty  and the software's author,  the holder of the   

economic rights,  and the successive licensors  have only  limited       

liability.                                                               

In this respect, the user's attention is drawn to the risks associated   

with loading,  using,  modifying and/or developing or reproducing the    

software by the user in light of its specific status of free software,   

that may mean  that it is complicated to manipulate,  and  that  also    

therefore means  that it is reserved for developers  and  experienced    

professionals having in-depth computer knowledge. Users are therefore    

encouraged to load and test the software's suitability as regards their  

requirements in conditions enabling the security of their systems and/or 

data to be ensured and,  more generally, to use and operate it in the    

same conditions as regards security.                                     

The fact that you are presently reading this means that you have had     

knowledge of the CeCILL license and that you accept its terms.           

Installation Instructions

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Links

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`NucleoMiner2` home page and documentation: https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer

Gael Yvert lab page: http://www.ens-lyon.fr/LBMC/gisv/

Installation

------------

 - Download archive

 - Compile bowtie2

 - Compile samtools

 - Compile bedtools

 - Compile TemplateFilter

Required R pacakes:

 - bot

   - fork

 - rjson

 - seqinr

.. code:: bash

  cd src/r_packages/

	tar xfvz R-latest.tar.gz 

	cd R-patched 

	./configure --with-x=no PDFLATEX="ls"

	make

  cd ../../..	

  R_BIN=src/r_packages/R-patched/bin/R 

	$R_BIN CMD INSTALL src/r_packages/rjson_0.2.12.tar.gz 

	$R_BIN CMD INSTALL src/r_packages/seqinr_3.0-7.tar.gz 

	$R_BIN CMD INSTALL src/r_packages/plotrix_3.4-5.tar.gz 

	$R_BIN CMD INSTALL src/r_packages/nm_2.0.tar.gz 

	$R_BIN CMD INSTALL src/r_packages/fork_1.2.4.tar.gz 

	$R_BIN CMD INSTALL src/r_packages/bot_0.9.tar.gz 

	$R_BIN CMD INSTALL src/r_packages/DESeq_1.14.0.tar.gz 

...

usage

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See html documentation for `NucleoMiner2`: http://www.ens-lyon.fr/LBMC/gisv/