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<!doctype html>
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<title>Virtual Laboratory for Plant Breeding Github Repository by vlpb3</title>
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<h1>Virtual Laboratory for Plant Breeding Github Repository</h1>
<p>This repository contains data analysis tools developed within Virtual Laboratory for Plant Breeding Project.</p>
<p class="view"><a href="https://github.com/vlpb3">View My GitHub Profile</a></p>
</header>
<section>
<h1 id="rna-seq-analysis-pipelines">
<a id="rna-seq-analysis-pipelines" class="anchor" href="#rna-seq-analysis-pipelines" aria-hidden="true"><span class="octicon octicon-link"></span></a>RNA-seq analysis pipelines</h1>
<p>Small RNA pipelines have beed developed within Virtual Laboratory for Plant Breeding projects. The pipelines make use of mostly R and Python. The diagram that has been used to build these pipelines:
<img src="Small_RNA_ pipeline_v2.png" alt="Diagram" style="width:420px;height:600px">
<p>
Currently the Basic QC, Mapping, Spike removal & visualization, normalization and pre- and post visualization are ready to use.
</p>
<p>Every pipeline is run in separate environment. By <em>encapsulating</em> most of the dependecies together with analysis code.</p>
<h2 id="different-levels-of-dependencies-">
<a id="different-levels-of-dependencies" class="anchor" href="#different-levels-of-dependencies" aria-hidden="true"><span class="octicon octicon-link"></span></a>Different levels of dependencies:</h2>
<h3 id="system-level-packages">
<a id="system-level-packages" class="anchor" href="#system-level-packages" aria-hidden="true"><span class="octicon octicon-link"></span></a>system level packages</h3>
<h3 id="python">
<a id="python" class="anchor" href="#python" aria-hidden="true"><span class="octicon octicon-link"></span></a>python</h3>
<ul>
<li>Python version</li>
<li>Python moudule versions </li>
</ul>
<p>both can be fixed with use of python virtual environment</p>
<h3 id="r">
<a id="r" class="anchor" href="#r" aria-hidden="true"><span class="octicon octicon-link"></span></a>R</h3>
<ul>
<li>R version</li>
<li>R packages version
the system level R version (first one in the path) is used</li>
</ul>
<p>Right versions of R packages are ensured with use of Packrat. That alows for building whole R environment with rigth R packages.<br>Packrat environment works at the level of directory.</p>
<pre><div># example basicQC analysis directory </div><div># with all necessary Packrat related files and directories </div><div>.</div><div>├── basicQC.htm # html file with QC report </div><div>├── basicQC.md # markdown file genereated by knitr </div><div>├── basicQC.Rmd # Rmarkdown defining the QC report </div><div>├── figure # plots </div><div>│ ├── A.design.plot-1.png</div><div>│ ├── C3plot-1.png</div><div>│ ├── D1plot-1.png</div><div>│ └── D2plot-1.png</div><div>├── get_experiment_fq.py # script that imports read data form sff files into fq files </div><div>├── packrat # dir with R environment related files </div><div>│ ├── init.R # script initializing Packrat environment </div><div>│ ├── lib # </div><div>│ ├── lib-ext # R library </div><div>│ ├── lib-R # </div><div>│ ├── packrat.lock # log of all the package versions used by this environment </div><div>│ ├── packrat.opts # packrat options </div><div>│ └── src</div><div>├── raw # fastq files generated from sff files </div><div>│ ├── N406T.fastq</div><div>│ ├── N540T.fastq</div><div>│ ├── N583T.fastq</div><div>│ └── sknas.fastq</div><div>├── README.md # project readme file </div><div>├── seqdesign.txt # experiment design file </div><div>└── Snakefile # pipeline defined for Snakemake </div></pre>
<h2 id="pipelines-and-tools-developed-at-university-of-amsterdam-">
<a id="pipelines-and-tools-developed-at-university-of-amsterdam" class="anchor" href="#pipelines-and-tools-developed-at-university-of-amsterdam" aria-hidden="true"><span class="octicon octicon-link"></span></a>Pipelines and tools developed at the University of Amsterdam:</h2>
<ul>
<li>
<h4 id="faradr">
<a id="faradr" class="anchor" href="#faradr" aria-hidden="true"><span class="octicon octicon-link"></span></a><a href="https://github.com/vlpb3/faradr">faradr</a></h4>
<p>R package used across the pipelines.</p>
</li>
<li>
<h4 id="basicqc">
<a id="basicqc" class="anchor" href="#basicqc" aria-hidden="true"><span class="octicon octicon-link"></span></a><a href="http://vlpb3.github.io/basicQC/">basicQC</a></h4>
<p>Quality control of raw reads in context of the experiment.</p>
</li>
<li>
<h4 id="rnaxcout">
<a id="rnaxcout" class="anchor" href="#rnaxcout" aria-hidden="true"><span class="octicon octicon-link"></span></a><a href="http://vlpb3.github.io/rnaxcount/">rnaxcount</a></h4>
<p>Alignment and counting fo small RNA species.</p>
</li>
<li>
<h4 id="rnaxqc">
<a id="rnaxqc" class="anchor" href="#rnaxqc" aria-hidden="true"><span class="octicon octicon-link"></span></a><a href="http://vlpb3.github.io/rnaxqc/">rnaxqc</a></h4>
<p>Quality control of small RNA counts in the context of the experiment.</p>
</li>
<li>
<h4 id="srna-norm">
<a id="srna-norm" class="anchor" href="#srna-norm" aria-hidden="true"><span class="octicon octicon-link"></span></a><a href="http://vlpb3.github.io/sRNA-norm/">sRNA-norm</a></h4>
<p>Normalisation for counts based on spike-in counts.</p>
</li>
</ul>
<h2 id="glossary-">
<a id="glossary" class="anchor" href="#glossary" aria-hidden="true"><span class="octicon octicon-link"></span></a>Glossary:</h2>
<dl>
<dt>Packrat</dt>
<dd>Packrat is a dependency management system for R.<a href="http://rstudio.github.io/packrat/"> Read more</a>.</dd>
<dt>Snakemake</dt>
<dd>Python module and library for building workflows. Project's aim is to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. <a href="https://bitbucket.org/johanneskoester/snakemake/wiki/Home">Read more</a>.</dd>
<dt>virtualenv</dt>
<dd>A tool to create isolated Python environments. See
<a href="http://virtualenv.readthedocs.org/en/latest/index.html"> Read more</a>.</dd>
</dl>
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