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software.html
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<?xml version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Software</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<meta name="copyright" content="[email protected]" />
<meta name="Description" content="Criao da sua imagem on-line" />
<meta name="Keywords"
content="bioconductor galaxy workflow4metabolomics"
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<meta name="author" content="[email protected]" />
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<body>
<div id="container">
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<div class="navcontainer">
<ul id="navlist">
<li><a href="index.html">Home</a></li>
<li><a href="research.html">Research</a></li>
<li><a href="publications.html">Publications</a></li>
<li><a href="projects.html">Projects</a></li>
<li><a href="team.html">Team</a></li>
<li><a href="training.html">Training</a></li>
<li><a href="software.html">Software</a></li>
<li><a href="jobs.html">Jobs</a></li>
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<p><strong>R packages</strong></p>
<ul>
<li><p><strong>biodb</strong>: a library and a development framework for connecting to chemical and biological databases (by Pierrick Roger; <a href="https://doi.org/doi:10.18129/B9.bioc.biodb">DOI:10.18129/B9.bioc.biodb</a>)</p></li>
<li><p><strong>biosigner</strong>: signature discovery from omics data (in collaboration with Philippe Rinaudo; <a href="https://doi.org/10.18129/B9.bioc.biosigner">DOI:10.18129/B9.bioc.biosigner</a>)</p></li>
<li><p><strong>phenomis</strong>: post-processing and univariate analysis of MS data (<a href="https://github.com/SciDoPhenIA/phenomis">https://github.com/SciDoPhenIA/phenomis</a>)</p></li>
<li><p><strong>proFIA</strong>: preprocessing of FIA-HRMS data (by Alexis Delabriere; <a href="https://doi.org/10.18129/B9.bioc.proFIA">DOI:10.18129/B9.bioc.proFIA</a>)</p></li>
<li><p><strong>ProMetIS</strong>: multi-omics phenotyping of the LAT and MX2 knockout mice (with Alyssa Imbert and the ProMetIS consortium; <a href="https://github.com/IFB-ElixirFr/ProMetIS">https://github.com/IFB-ElixirFr/ProMetIS</a>)</p></li>
<li><p><strong>ptairMS</strong>: Pre-processing PTR-TOF-MS Data (by Camille Roquencourt; <a href="https://doi.org/10.18129/B9.bioc.ptairMS">DOI:10.18129/B9.bioc.ptairMS</a>)</p></li>
<li><p><strong>ropls</strong>: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data (<a href="https://doi.org/10.18129/B9.bioc.ropls">DOI:10.18129/B9.bioc.ropls</a>)</p></li>
</ul>
<p><strong>Datasets; <a href="http://www.ebi.ac.uk/metabolights/index">MetaboLights</a> repository</strong></p>
<ul>
<li><p><a href="https://www.ebi.ac.uk/metabolights/MTBLS1903">MTBLS1903</a>: ProMetIS: deep phenotyping of knock-out mice by proteomics and metabolomics.</p></li>
<li><p><a href="https://www.ebi.ac.uk/metabolights/MTBLS404">MTBLS404</a>: Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses ('Sacurine' data set).</p></li>
<li><p><a href="https://www.ebi.ac.uk/metabolights/MTBLS148">MTBLS148</a>: Impact of collection conditions on the metabolite content of human urine samples as analyzed by liquid chromatography coupled to mass spectrometry and nuclear magnetic resonance spectroscopy.</p></li>
</ul>
<p><strong>Galaxy modules; <a href="https://toolshed.g2.bx.psu.edu">Galaxy</a> toolshed</strong></p>
<ul>
<li><p>Batch Correction (in collaboration with Jean-Francois Martin, Melanie Petera, Marion Landi and Franck Giacomoni)</p></li>
<li><p>Biosigner (in collaboration with Philippe Rinaudo)</p></li>
<li><p>Heatmap</p></li>
<li><p>Multivariate</p></li>
<li><p>proFIA (in collaboration with Alexis Delabriere)</p></li>
<li><p>Quality Metrics (in collaboration with Melanie Petera)</p></li>
<li><p>Univariate (in collaboration with Marie Tremblay-Franco)</p></li>
</ul>
<p><strong>Workflows and histories; <a href="http://workflow4metabolomics.org/referenced_W4M_histories">Workflow4Metabolomics</a> e-infrastructure</strong></p>
<ul>
<li><p>W4M00001_Sacurine-statistics (<a href="http://dx.doi.org/10.15454/1.4811121736910142E12">DOI:10.15454/1.4811121736910142E12</a>)</p></li>
<li><p>W4M00002_Sacurine-comprehensive (<a href="http://dx.doi.org/10.15454/1.481114233733302E12">DOI:10.15454/1.481114233733302E12</a>)</p></li>
<li><p>W4M00003_Diaplasma (<a href="http://dx.doi.org/10.15454/1.4811165052113186E12">DOI:10.15454/1.4811165052113186E12</a>)</p></li>
</ul>
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