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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<title>Statistics with RStudio</title>
<link rel="stylesheet" href="stylesheets/styles.css">
<link rel="stylesheet" href="stylesheets/github-light.css">
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
<!--[if lt IE 9]>
<script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
</head>
<body>
<div class="wrapper">
<header>
<h1>Statistics with RStudio</h1>
<p>This repository contains the teaching material for the introductory course <b>NGS Statistics with R</b>, developed for the <a target="_blank" href="https://www.france-bioinformatique.fr/fr/evenements/EBA2016">Aviesan Bioinformatics School (Ecole de Bioinformatique Aviesan)</a> -- Roscoff (France)</p>
<p>This course has been conceived to provide life science researchers and engineers with a first contact to statistical analysis of NGS data using the statistical package <b><a target="_blank" href="https://www.r-project.org/">R</a></b>, under the <a target="_blank" href="https://www.rstudio.com/">RStudio</a> environment.</p>
<p class="view"><a href="http://jvanheld.github.io/stats_avec_RStudio_EBA/">View the Web course</a><br><small><a href="http://jvanheld.github.io/stats_avec_RStudio_EBA/">http://jvanheld.github.io/stats_avec_RStudio_EBA/</a></small>
<ul>
<li><a href="https://github.com/jvanheld/EBA15_stats_RStudio/zipball/master">Download <strong>ZIP File</strong></a></li>
<li><a href="https://github.com/jvanheld/EBA15_stats_RStudio/tarball/master">Download <strong>TAR Ball</strong></a></li>
<li><a href="https://github.com/jvanheld/EBA15_stats_RStudio">View On <strong>GitHub</strong></a></li>
</ul>
</header>
<section>
<h3><a id="resources" class="anchor" href="#resources" aria-hidden="true"><span class="octicon octicon-link"></span></a>Resources</h3>
<table>
<tr>
<td><a target="_blank" href="http://www.rstudio.com/"><b>RStudio</b></a></td>
<td>
<a target="_blank" href="https://www.rstudio.com/">https://www.rstudio.com/</a>
<br>[<a target="_blank" href="https://www.rstudio.com/products/RStudio/#Desktop">Download RStudio desktop</a>]
</td>
</tr>
<tr>
<td><b>RStudio</b> VM at IFB cloud</td>
<td><a target="_blank" href="http://cloud.france-bioinformatique.fr/cloud/">http://cloud.france-bioinformatique.fr/cloud/</a>
<small>
<br>Open an instance of <b>R statistical computing (2016-02)</b>
<br>(login/passwd: ruser/ruser)
</small>
</td>
</tr>
<tr>
<td><b>R and RStudio Cheat Sheets</b></td>
<td><a target="_blank" href="https://www.rstudio.com/resources/cheatsheets/">https://www.rstudio.com/resources/cheatsheets/</a></td>
</tr>
<!--
<tr>
<td><a target="_blank" href="http://cloud.france-bioinformatique.fr/"><b>IFB cloud</b></a></td>
<td><a target="_blank" href="http://cloud.france-bioinformatique.fr/">http://cloud.france-bioinformatique.fr/</a></a></td>
</tr>
-->
</table>
<h3>
<a id="doc" class="anchor" href="#doc" aria-hidden="true"><span class="octicon octicon-link"></span></a>Documents</h3>
<ol>
<li>R - bash bilinguism
[<a target='_blank' href='slides/R-bash/R_and_bash_bilinguism.html'>html</a>]
[<a target='_blank' href='slides/R-bash/R_and_bash_bilinguism.pdf'>pdf</a>]
<small>[<a target='_blank' href='slides/R-bash/R_and_bash_bilinguism.Rmd'>Rmd</a>]</small>
</li>
</ol>
<h3>
<a id="practicals" class="anchor" href="#practicals" aria-hidden="true"><span class="octicon octicon-link"></span></a>Practicals</h3>
<ol>
<li>Opening an RStudio session
[<a target='_blank' href='practicals/00_RStudio_environment/RStudio_environment.html'>html</a>]
[<a target='_blank' href='practicals/00_RStudio_environment/RStudio_environment.pdf'>pdf</a>]
<!-- [<a target='_blank' href='practicals/00_RStudio_environment/RStudio_environment.pdf'>pdf</a>]-->
<small>[<a target='_blank' href='practicals/00_RStudio_environment/RStudio_environment.Rmd'>Rmd</a>]</small>
</li>
<li>First steps with R
[<a target='_blank' href='practicals/01_first_steps_with_R/01_first_steps_with_R.html'>html</a>]
[<a target='_blank' href='practicals/01_first_steps_with_R/01_first_steps_with_R.pdf'>pdf</a>]
[<a target='_blank' href='practicals/01_first_steps_with_R/01_first_steps_with_R.R'>R code</a>]
<small>[<a target='_blank' href='practicals/01_first_steps_with_R/01_first_steps_with_R.Rmd'>Rmd</a>]</small>
</li>
<li>R in 1h45 (Hugo Varet)
[<a target='_blank' href='practicals/2018_R-en-45-minutes/slides_intro_R_2018.html'>html</a>]
[<a target='_blank' href='practicals/2018_R-en-45-minutes/slides_intro_R_2018.pdf'>pdf</a>]
[<a target='_blank' href='practicals/2018_R-en-45-minutes/slides_intro_R_2018.Rmd '>R code</a>]
<small>[<a target='_blank' href='practicals/2017_R-en-45-minutes/intro_R_Roscoff.Rmd'>Rmd</a>]</small>
</li>
<li>GTF file exercise (Hugo Varet)
<small>[<a target='_blank' href='practicals/2017_R-en-45-minutes/correction_exo_GTF.r'>R code</a>]</small>
</li>
<li>ChIP-seq peak-calling: tutorial
[<a target='_blank' href='practicals/02_peak-calling/peak-calling_stats_practical.html'>html</a>]
[<a target='_blank' href='practicals/02_peak-calling/peak-calling_stats_practical.pdf'>pdf</a>]
[<a target='_blank' href='practicals/02_peak-calling/peak-calling_stats_practical.R'>R code</a>]
<small>[<a target='_blank' href='practicals/02_peak-calling/peak-calling_stats_practical.Rmd'>Rmd</a>]</small>
</li>
<li>ChIP-seq peak-calling: commented report
[<a target='_blank' href='practicals/02_peak-calling/peak-calling_report.html'>html</a>]
[<a target='_blank' href='practicals/02_peak-calling/peak-calling_report.pdf'>pdf</a>]
[<a target='_blank' href='practicals/02_peak-calling/peak-calling_report.R'>R code</a>]
<small>[<a target='_blank' href='practicals/02_peak-calling/peak-calling_report.Rmd'>Rmd</a>]</small>
</li>
<li>Exploring RNA-seq counts
[<a target='_blank' href='practicals/03_exploring_rnaseq_counts/exploring_RNASeq_counts.html'>html</a>]
[<a target='_blank' href='practicals/03_exploring_rnaseq_counts/exploring_RNASeq_counts.pdf'>pdf</a>]
[<a target='_blank' href='practicals/03_exploring_rnaseq_counts/exploring_RNASeq_counts.R'>R code</a>]
<small>[<a target='_blank' href='practicals/03_exploring_rnaseq_counts/exploring_RNASeq_counts.Rmd'>Rmd</a>]</small>
</li>
</ol>
<h3><a id="authors-and-contributors" class="anchor" href="#authors-and-contributors" aria-hidden="true"><span class="octicon octicon-link"></span></a>Authors and Contributors</h3>
<ul>
<li>Jacques van Helden (<a href="https://github.com/jvanheld" class="user-mention">@jvanheld</a>)</li>
<li>Hugo Varet (<a href="https://github.com/hvaret" class="user-mention">@hvaret</a>)</li>
<li>Julie Aubert (<a href="https://github.com/julieaubert" class="user-mention">@julieaubert</a>)</li>
</ul>
<h4>Co-teachers</h4>
<ul>
<li>Denis Puthier (<a href="https://github.com/dputhier" class="user-mention">@dputhier</a>)</li>
<!-- <li>Carl Herrmann (<a href="https://github.com/carlherrmann" class="user-mention">@carlherrmann</a>)</li>-->
<li>Matthieu Defrance (<a href="https://github.com/epinomics" class="user-mention">@epinomics</a>)</li>
</ul>
<h4>
<a id="contact" class="anchor" href="#contact" aria-hidden="true"><span class="octicon octicon-link"></span></a>Contact</h4>
<p>Jacques van Helden (<a href="mailto:Jacques.van-Helden@univ-amu.fr" class="user-mention">Jacques.van-Helden@univ-amu.fr</a>).</p>
</section>
<footer>
<p>This project is maintained by <a href="https://github.com/jvanheld">jvanheld</a></p>
<p><small>Hosted on GitHub Pages — Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
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