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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<title>Urpp tutorials by milchmolch</title>
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<body>
<div class="wrapper">
<header>
<h1>Urpp tutorials</h1>
<p></p>
<p class="view"><a href="https://github.com/milchmolch/URPP_Tutorials">View the Project on GitHub <small>milchmolch/URPP_Tutorials</small></a></p>
<ul>
<li><a href="https://github.com/milchmolch/URPP_Tutorials/zipball/master">Download <strong>ZIP File</strong></a></li>
<li><a href="https://github.com/milchmolch/URPP_Tutorials/tarball/master">Download <strong>TAR Ball</strong></a></li>
<li><a href="https://github.com/milchmolch/URPP_Tutorials">View On <strong>GitHub</strong></a></li>
</ul>
</header>
<section>
<h1>
<a id="urpp-tutorials" class="anchor" href="#urpp-tutorials" aria-hidden="true"><span class="octicon octicon-link"></span></a>URPP Tutorials</h1>
<h2>
<a id="urpp-evolution-in-action" class="anchor" href="#urpp-evolution-in-action" aria-hidden="true"><span class="octicon octicon-link"></span></a>URPP Evolution in Action</h2>
<p>Stefan Wyder & Heidi Lischer</p>
<h2>
<a id="linuxbash-shell-3-parts-3x3h9h" class="anchor" href="#linuxbash-shell-3-parts-3x3h9h" aria-hidden="true"><span class="octicon octicon-link"></span></a>Linux/Bash shell (3 parts, 3x3h=9h)</h2>
<ol>
<li>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Tutorial_LinuxPart1.pdf"><strong>Basics 1</strong></a><br>
Folder structure, commands with files&folders, commands with text, piping, (awk)<br>
<a href="http://milchmolch.github.io/URPP_Tutorials/LinuxShell/Unix_Part1.html">Hands-on</a>
</li>
<li>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Tutorial_LinuxPart2.pdf"><strong>Basics 2</strong></a><br>
ssh, compression, permission, (bash scripting)<br>
<a href="http://milchmolch.github.io/URPP_Tutorials/LinuxShell/Unix_Part2.html">Hands-on</a><br>
</li>
<li>
<strong>Intermediate</strong><br>
<ul>
<li>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Tutorial_LinuxPart3_HL.pdf">bash scripting</a> | <a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/Exercises_LinuxPart3_HL.pdf">Exercises</a>
</li>
<li>
<a href="https://github.com/milchmolch/URPP_Tutorials/blob/master/LinuxShell/URPP_Tutorial_LinuxPart3_SW.pdf">parallel jobs, awk, regexps</a> | <a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Hands-on_UnixPart3_SW.pdf">Hands-on</a><br>
</li>
</ul>
</li>
</ol>
<h2>
<a id="next-generation-sequencing-4-parts-4x3h12h" class="anchor" href="#next-generation-sequencing-4-parts-4x3h12h" aria-hidden="true"><span class="octicon octicon-link"></span></a>Next-Generation-Sequencing (4 parts, 4x3h=12h)</h2>
<ol>
<li>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part1.pdf"><strong>Introduction</strong></a><br>
Sequencing Technologies, Quality control (FastQC), SAM/BAM formats, samtools<br>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Hands-on_NGS_Part1.pdf">Hands-on</a><br>
</li>
<li>
<a href="http://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part2.pdf"><strong>Variant Calling</strong></a><br>
Preprocessing BAMs, variant calling example (freebayes), VCF format<br>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Hands-on_NGS_Part2.pdf">Hands-on</a>
</li>
<li>
<strong>Variant Calling 2</strong><br>
variant calling (GATK), Variant Effect Prediction<br>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part3_HL.pdf">Theory 1</a> | <a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part3_SW.pdf">Theory 2</a> | <a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Exercises_NGS_Part3.pdf">Hands-on</a>
</li>
<li>
<strong>RNA-seq & Making sense of gene lists</strong><br>
Differential expression (edgeR), Gene Ontology Analysis, Gene Set Enrichment Analysis<br>
<a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_RNAseq_HL.pdf">Theory 1</a> | <a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_RNAseq_SW.pdf">Theory 2</a> | <a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/Exercises_RNAseq_Tutorial_HL.pdf">Hands-on 1</a> | <a href="https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/Exercises_RNAseq_Tutorial_SW.pdf">Hands-on 2</a>
</li>
</ol>
<h2>
<a id="r-3-parts-2x65h3h15h" class="anchor" href="#r-3-parts-2x65h3h15h" aria-hidden="true"><span class="octicon octicon-link"></span></a>R (3 parts, 2x6.5h+3h=15h)</h2>
<ol>
<li>
<strong>Introduction into R</strong><br>
Using R as a calculator, variables, subsetting, reading in data, writing functions, apply functions, missing data, plotting (base::plot)</li>
<li>
<strong>Programming Exercises</strong><br>
Plotting using ggplot2, writing clean code, programming exercises</li>
<li>
<strong>Programming Exercises 2</strong><br>
Repetition (programming structures, clean coding, project organization)</li>
</ol>
<p><a href="http://milchmolch.github.io/R_Tutorial/">Stefan's website</a></p>
<p><a href="">Heidi's material (pdf documents)</a></p>
<h2>
<a id="user-content-introduction-to-python" class="anchor" href="#introduction-to-python" aria-hidden="true"><span class="octicon octicon-link"></span></a>Introduction to python (2 parts)</h2>
<ol>
<li>
<strong>Basics</strong><br>
Basics, control flow, lists, file input/output, writing function, dictionaries, tuples, sets</li>
<li>
<strong>Basics 2</strong>*<br>
object-oriented programming, BioPython, regular expressions</li>
</ol>
<p><a href="http://github.com/milchmolch/Python_Tutorial/">Stefan's website</a> </p>
</section>
<footer>
<p>This project is maintained by <a href="https://github.com/milchmolch">milchmolch</a></p>
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