Révision e5603c3f README
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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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quantitative analysis of epigenetic marks on individual nucleosomes.
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It was developed to detect natural Single-Nucleosome Epi-Polymorphisms
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(SNEP) from MNase-seq and ChIP-seq data.
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License |
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of the economic rights, and the successive licensors have only |
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limited 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 |
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their requirements in conditions enabling the security of their |
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systems and/or data to be ensured and, more generally, to use and |
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operate it in the same conditions as regards security. |
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This software is provided with absolutely NO WARRANTY. The authors can |
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not be held responsible, even partially, for any damage, loss, |
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financial loss or any other undesired facts resulting from the use of |
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the software. In this respect, the user's attention is drawn to the |
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risks associated with loading, using, modifying and/or developing or |
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reproducing the software by the user in light of its specific status |
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of free software, that may mean that it is complicated to manipulate, |
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and that also therefore means that it is reserved for developers |
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and experienced professionals having in-depth computer knowledge. |
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Users are therefore encouraged to load and test the software's |
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suitability as regards their requirements in conditions enabling the |
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security of their systems and/or data to be ensured and, more |
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generally, to use and operate it in the same conditions as regards |
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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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Links |
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*NucleoMiner2* home page and documentation: https://forge.cbp.ens- |
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lyon.fr/redmine/projects/nucleominer |
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*NucleoMiner2* home page and documentation are available here: |
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Gael Yvert lab page: http://www.ens-lyon.fr/LBMC/gisv/ |
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* https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer |
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The Yvert lab web page is accessible here: |
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* 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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Prerequisites |
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~~~~~~~~~~~~~ |
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To work properly, NucleoMiner2 needs that the following free software |
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are installed and made available on your system: |
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* Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2 |
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* Compile samtools
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* SAMtools http://samtools.sourceforge.net
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* Compile bedtools
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* bedtools http://code.google.com/p/bedtools/
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* Compile TemplateFilter |
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* TemplateFilter |
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http://compbio.cs.huji.ac.il/NucPosition/TemplateFiltering |
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Required R packages:
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* bot
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It also requires the following R packages to be installed on your
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system:
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* fork |
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* seqinr |
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* cachecache |
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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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* cachecache https://forge.cbp.ens- |
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lyon.fr/redmine/projects/cachecache |
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usage |
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===== |
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* bot https://forge.cbp.ens-lyon.fr/redmine/projects/bot |
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See html documentation for *NucleoMiner2*: http://www.ens- |
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lyon.fr/LBMC/gisv/ |
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* nucleominer https://forge.cbp.ens- |
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lyon.fr/redmine/projects/nucleominer |
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Formats disponibles : Unified diff