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{"name":"Virtual Laboratory for Plant Breeding Github Repository","tagline":"This repository contains data analysis tools developed within Virtual Laboratory for Plant Breeding Project.","body":"<h1 id=\"rna-seq-analysis-pipelines\">RNA-seq analysis pipelines</h1>\r\n<p>Small RNA pipelines have beed developed within Virtual Laboratory for Plant Breeding projects. They are mostly used with R and Python.</p>\r\n<p>Every pipeline is run in separate environment. By <em>encapsulating</em> most of the dependecies together with analysis code.</p>\r\n<h2 id=\"different-levels-of-dependencies-\">Different levels of dependencies:</h2>\r\n<h3 id=\"system-level-packages\">system level packages</h3>\r\n<h3 id=\"python\">python</h3>\r\n<ul>\r\n<li>Python version</li>\r\n<li>Python moudule versions </li>\r\n</ul>\r\n<p>both can be fixed with use of python virtual environment</p>\r\n<h3 id=\"r\">R</h3>\r\n<ul>\r\n<li>R version</li>\r\n<li>R packages version\r\nthe system level R version (first one in the path) is used</li>\r\n</ul>\r\n<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>\r\n<pre class=\"editor-colors lang-sh\"><div class=\"line\"><span class=\"source shell\"><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> example basicQC analysis directory</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> with all necessary Packrat related files and directories</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span class=\"support function builtin shell\"><span>.</span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── basicQC.htm </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> html file with QC report</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── basicQC.md </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> markdown file genereated by knitr</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── basicQC.Rmd </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> Rmarkdown defining the QC report</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── figure </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> plots</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── A.design.plot-1.png</span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── C3plot-1.png</span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── D1plot-1.png</span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ └── D2plot-1.png</span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── get_experiment_fq.py </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> script that imports read data form sff files into fq files</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── packrat </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> dir with R environment related files</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── init.R </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> script initializing Packrat environment</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── lib </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── lib-ext </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> R library</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── lib-R </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── packrat.lock </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> log of all the package versions used by this environment</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── packrat.opts </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> packrat options</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ └── src</span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── raw </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> fastq files generated from sff files</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── N406T.fastq</span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── N540T.fastq</span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ ├── N583T.fastq</span></span></div><div class=\"line\"><span class=\"source shell\"><span>│ └── sknas.fastq</span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── README.md </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> project readme file</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>├── seqdesign.txt </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> experiment design file</span><span> </span></span></span></div><div class=\"line\"><span class=\"source shell\"><span>└── Snakefile </span><span class=\"comment line number-sign shell\"><span class=\"punctuation definition comment shell\"><span>#</span></span><span> pipeline defined for Snakemake</span><span> </span></span></span></div></pre>\r\n<h2 id=\"pipelines-and-tools-developed-at-university-of-amsterdam-\">Pipelines and tools developed at University of Amsterdam:</h2>\r\n<ul>\r\n<li><h4 id=\"faradr\">faradr</h4>\r\n<p>R package used across the pipelines.</p>\r\n</li>\r\n<li><h4 id=\"basicqc\">basicQC</h4>\r\n<p>Quality control of raw reads in context of the experiment.</p>\r\n</li>\r\n<li><h4 id=\"rnaxcout\">rnaxcout</h4>\r\n<p>Alignment and counting fo small RNA species.</p>\r\n</li>\r\n<li><h4 id=\"rnaxqc\">rnaxqc</h4>\r\n<p>Quality control of small RNA counts in the context of the experiment.</p>\r\n</li>\r\n<li><h4 id=\"srna-norm\">sRNA-norm</h4>\r\n<p>Normalisation for counts based on spike-in counts.</p>\r\n</li>\r\n</ul>\r\n<h2 id=\"glossary-\">Glossary:</h2>\r\n<dl>\r\n <dt>Packrat</dt>\r\n <dd>Packrat is a dependency management system for R.<a href=\"http://rstudio.github.io/packrat/\"> Read more</a>.</dd>\r\n\r\n <dt>Snakemake</dt>\r\n <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>\r\n\r\n <dt>virtualenv</dt>\r\n <dd>A tool to create isolated Python environments. See\r\n <a href=\"http://virtualenv.readthedocs.org/en/latest/index.html\"> Read more</a>.</dd>\r\n\r\n</dl>","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}