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<!DOCTYPE html>
<html lang="en-us">
<head>
<meta charset="UTF-8">
<title>Reproducible-r by MRC LMS</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="stylesheets/normalize.css" media="screen">
<link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
<link rel="stylesheet" type="text/css" href="stylesheets/stylesheet.css" media="screen">
<link rel="stylesheet" type="text/css" href="stylesheets/github-light.css" media="screen">
</head>
<body>
<section class="page-header">
<h1 class="project-name">Reproducible-r</h1>
<h2 class="project-tagline">Course - Introduction to R and reproducible research in R</h2>
<a href="https://github.com/LMSBioinformatics/LMS_Reproducible-R" class="btn">View on GitHub</a>
<a href="https://github.com/LMSBioinformatics/LMS_Reproducible-R/zipball/master" class="btn">Download .zip</a>
<a href="https://github.com/LMSBioinformatics/LMS_Reproducible-R/tarball/master" class="btn">Download .tar.gz</a>
</section>
<section class="main-content">
<h1>
<a id="reproducible-research-in-r" class="anchor" href="#reproducible-research-in-r" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Reproducible Research in R</h1>
<h2>
<a id="the-course" class="anchor" href="#the-course" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>The Course</h2>
<p>This course introduces R and statistical programming as well as best practices for reproducible research using R's dynamic reporting and version capture tools.</p>
<p>The course consists of 3 sections, 2 on basic R and 1 on reproducibility in R.<br>
Each section is presented as both HTMl and Rpres markdown ( to allow for intergration of the presentation in the RStudion enviroment itself). Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples. </p>
<p>Course material and exercises are available to view as rendered HTML at <a href="https://lmsbioinformatics.github.io/LMS_Reproducible-R/">https://lmsbioinformatics.github.io/LMS_Reproducible-R/</a>.<br>
All material is available to download under GPL v2 license.</p>
<p>For information on other courses run by our team see our <a href="https://lmsbioinformatics.github.io/MRCLMSBioinfo/LMStraining.html">github IO page</a>.</p>
<h2>
<a id="the-team" class="anchor" href="#the-team" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>The Team</h2>
<p>This course was created and conducted by the MRC London Institute of Medical Sciences Bioinformatics Team at Imperial College London, Hammersmith Hospital.<br>
For more information on the team see our <a href="https://lmsbioinformatics.github.io/MRCLMSBioinfo/LMStraining.html">github IO page</a>.</p>
<p>This course is free for MRC LMS and Imperial staff and students. If you would like to attend a future course contact <a href="mailto:[email protected]">Contact Us</a>.</p>
<h2>
<a id="setting-up" class="anchor" href="#setting-up" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Setting up.</h2>
<h4>
<a id="install-r" class="anchor" href="#install-r" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Install R.</h4>
<p>R can be installed from the R-project website.<br>
R 3.1.0 or higher is required for this course.</p>
<p><a href="http://www.r-project.org/">http://www.r-project.org/</a></p>
<h4>
<a id="install-rstudio" class="anchor" href="#install-rstudio" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Install RStudio.</h4>
<p>RStudio can be installed from the R-project website. </p>
<p><a href="http://www.rstudio.com/">http://www.rstudio.com/</a></p>
<h4>
<a id="install-required-packages" class="anchor" href="#install-required-packages" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Install required packages.</h4>
<h5><b>Option 1 - (For your own personal computers)</b></h5>
<p>Having downloaded R and RStudio, some additional packages are required (rmarkdown and ggplot2).<br>
To install these,</p>
<ul>
<li>First launch RStudio</li>
<li>Install the packages in the R console using devtools
<pre>
install.packages("devtools",dependencies=TRUE)
devtools::install_github("LMSBioinformatics/Reproducible-R",subdir="reproducibleR",build_vignettes=TRUE)
</pre>
</li>
</ul>
<<<<<<< HEAD
<h5><b>Option 2 - (For Imperial Hammersmith library)</b></h5>
=======
<h5><b>Option 2 - (For Imperial Hammersmith library)</b></h5>
>>>>>>> .
<p>Having downloaded R and RStudio, some additional packages are required (rmarkdown and ggplot2).<br>
To install these,</p>
<ul>
<li>First launch RStudio</li>
<<<<<<< HEAD
<li>Install the packages in the R console using install.packages
=======
<li>Install the packages in the R console using install.packages
>>>>>>> .
<pre>
install.packages("ggplot2",dependencies=TRUE)
install.packages("rmarkdown",dependencies=TRUE)
install.packages("yaml",dependencies=TRUE)
</pre>
</li>
</ul>
<h4>
<a id="download-the-material" class="anchor" href="#download-the-material" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Download the material</h4>
<p>The material can either be downloaded as a <a href="https://github.com/LMSBioinformatics/LMS_Reproducible-R/archive/master.zip/archive/master.zip">zip</a></p>
<pre>
wget https://github.com/LMSBioinformatics/LMS_Reproducible-R/archive/master.zip/archive/master.zip ./
</pre>
<p>or checked out from our Github repository
<a href="https://github.com/LMSBioinformatics/LMS_Reproducible-R">https://github.com/LMSBioinformatics/LMS_Reproducible-R/</a></p>
<h2>
<a id="the-r-sessions" class="anchor" href="#the-r-sessions" aria-hidden="true"><span class="octicon octicon-link"></span></a>The R Sessions</h2>
<h4>
<a id="Session1" class="anchor" href="#session1" aria-hidden="true"><span class="octicon octicon-link"></span></a>Introduction to R, Session 1</h4>
<p>This section focuses on R basics such as simple data types, data IO, plotting and statistics.<br>
Session sections:
<ul>
<li>Introduction to R</li>
<li>Data Types</li>
<li>Reading and Writing Data</li>
<li>Plotting</li>
<li>Statistics</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/introToR_Session1.html">Session 1</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/introToR_Session1.html">Session 1</a><br>
Link to R code included in presentation- - <a href="./r_course/presentations/rcode/introToR_Session1.R">Session 1</a><br>
<iframe src="./r_course/presentations/slides/introToR_Session1.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session2" class="anchor" href="#session2" aria-hidden="true"><span class="octicon octicon-link"></span></a>Introduction to R, Session 2</h4>
<p>In session 2, programmatic techniques such as looping and use defined functions are introduced<br>
The session includes longer exercises and shorter slide decks and so more time should be allocated to exercises in this session.<br>
Session sections:
<ul>
<li>Looping Conditional Branching</li>
<li>Data Types</li>
<li>Writing Scripts</li>
<li>Getting</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/presentations/slides/introToR_Session2.html">Session 2</a><br>
Link to single page, printable HTML - <a href="./r_course/presentations/singlepage/introToR_Session2.html">Session 2</a><br>
Link to R code included in presentation- - <a href="./r_course/presentations/rcode/introToR_Session2.R">Session 2</a><br>
<iframe src="./r_course/presentations/slides/introToR_Session2.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="Session2" class="anchor" href="#session2" aria-hidden="true"><span class="octicon octicon-link"></span></a>Introduction to R, Session 2: Loading Libraries</h4>
<p>In this session, the concept of libraries is introduced and how to install and load them is described.
<ul>
<li>Libraries and repositories</li>
<li>Install R packages from CRAN</li>
<li>Installing R packages from Bioconductor</li>
<li>Getting help about the packages</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/loading_libraries/loading_libraries_slides.html">Session 2</a><br>
Link to single page, printable HTML - <a href="./r_course/loading_libraries/loading_libraries_singlePage.html">Session 2</a><br>
<iframe src="./r_course/loading_libraries/loading_libraries_slides.html" width="100%" height="400"></iframe>
</span>
<h4>
<a id="reproducible-r" class="anchor" href="#reproducible-r" aria-hidden="true"><span class="octicon octicon-link"></span></a>Introduction to R, Session 3: Reproducible Reporting in R</h4>
<p>In the Reproducible Reporting in R session, the use of dynamic documents is introduced with topics such as Markdown syntax, YAML headers and rmarkdown/knitr documen rendering functions<br>
Session sections:
<ul>
<li>Creating reports from R scripts</li>
<li>Markdown Syntax</li>
<li>Markdown in R</li>
</ul>
</p>
Link to HTML presentation - <a href="./r_course/reproducibleR_slides.html">Session 3</a><br>
Link to single page, printable HTML - <a href="./r_course/reproducibleR.html">Session 3</a><br>
Link to R code included in presentation- - <a href="./r_course/reproducibleR.Rpres">Session 3</a><br>
<iframe src="./r_course/reproducibleR_slides.html" width="100%" height="400"></iframe>
<p>
</p>
</span>
<footer class="site-footer">
<span class="site-footer-owner"><a href="https://github.com/LMSBioinformatics/LMS_Reproducible-R">Reproducible-r</a> is maintained by <a href="https://github.com/LMSBioinformatics">MRC LMS </a>.</span>
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