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Readme / Documentation for `NucleoMiner2` |
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`NucleoMiner2` offers Python API and R package allowing to perform |
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quantitative analysis of nucleosomal epigenome. It is especially well |
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suited for scripting to extract natural Single-Nucleosome Epi- |
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Polymorphisms (SNEP) from ChIP-Seq data. |
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License |
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======= |
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Copyright CNRS 2012-2013 |
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- Florent CHUFFART |
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- Jean-Baptiste VEYRIERAS |
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- Gael YVERT |
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This software is a computer program which purpose is to perform quanti- |
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tative analysis of epigenetic marks at single nucleosome resolution. |
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This software is governed by the CeCILL license under French law and |
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abiding by the rules of distribution of free software. You can use, |
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modify and/ or redistribute the software under the terms of the CeCILL |
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license as circulated by CEA, CNRS and INRIA at the following URL |
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"http://www.cecill.info". |
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As a counterpart to the access to the source code and rights to copy, |
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modify and redistribute granted by the license, users are provided only |
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with a limited warranty and the software's author, the holder of the |
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economic rights, and the successive licensors have only limited |
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liability. |
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In this respect, the user's attention is drawn to the risks associated |
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with loading, using, modifying and/or developing or reproducing the |
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software by the user in light of its specific status of free software, |
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that may mean that it is complicated to manipulate, and that also |
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therefore means that it is reserved for developers and experienced |
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professionals having in-depth computer knowledge. Users are therefore |
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encouraged to load and test the software's suitability as regards their |
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requirements in conditions enabling the security of their systems and/or |
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data to be ensured and, more generally, to use and operate it in the |
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same conditions as regards security. |
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The fact that you are presently reading this means that you have had |
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knowledge of the CeCILL license and that you accept its terms. |
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Installation Instructions |
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========================= |
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Links |
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----- |
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`NucleoMiner2` home page and documentation: https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer |
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Gael Yvert lab page: http://www.ens-lyon.fr/LBMC/gisv/ |
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Installation |
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------------ |
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- Download archive |
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- Compile bowtie2 |
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- Compile samtools |
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- Compile bedtools |
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- Compile TemplateFilter |
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Required R packages: |
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- bot |
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- fork |
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- rjson |
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- seqinr |
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- cachecache |
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.. code:: bash |
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cd src/r_packages/ |
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tar xfvz R-latest.tar.gz |
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cd R-patched |
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./configure --with-x=no PDFLATEX="ls" |
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make |
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cd ../../.. |
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R_BIN=src/r_packages/R-patched/bin/R |
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$R_BIN CMD INSTALL src/r_packages/rjson_0.2.12.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/seqinr_3.0-7.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/plotrix_3.4-5.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/nm_2.0.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/fork_1.2.4.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/bot_0.9.tar.gz |
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$R_BIN CMD INSTALL src/r_packages/DESeq_1.14.0.tar.gz |
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... |
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usage |
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===== |
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See html documentation for `NucleoMiner2`: http://www.ens-lyon.fr/LBMC/gisv/ |