r-intermediate/index.html at master · ThomasCarroll/r-intermediate · GitHub

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<!doctype html>
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    <title>Data Manipulation and Visualisation using R by bioinformatics-core-shared-training</title>

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        <h1>Data Manipulation and Visualisation using R</h1>
        <p>Intermediate R Course</p>

        <p class="view"><a href="https://github.com/bioinformatics-core-shared-training/r-intermediate">View the Project on GitHub <small>bioinformatics-core-shared-training/r-intermediate</small></a></p>


        <ul>
          <li><a href="https://github.com/bioinformatics-core-shared-training/r-intermediate/zipball/master">Download <strong>ZIP File</strong></a></li>
          <li><a href="https://github.com/bioinformatics-core-shared-training/r-intermediate/tarball/master">Download <strong>TAR Ball</strong></a></li>
          <li><a href="https://github.com/bioinformatics-core-shared-training/r-intermediate">View On <strong>GitHub</strong></a></li>
        </ul>
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      <section>
        <img src="https://raw.githubusercontent.com/bioinformatics-core-shared-training/r-intermediate/master/images/data-cycle.png">
<h2>
<a id="course-description" class="anchor" href="#course-description" aria-hidden="true"><span class="octicon octicon-link"></span></a>Course Description</h2>
It has been said that 80% of data analysis is spent on the process of cleaning and preparing the data. In this course we introduce some relatively-new additions to the R programming language; dplyr and ggplot2. In combination these provide a powerful toolkit to make the process of manipulating and visualising data easy and intuitive.
<br>
<h2>
<a id="prereq" class="anchor" href="#prereq" aria-hidden="true"><span class="octicon octicon-link"></span></a>Course Prequisites</h2>
We will assume that you have basic familarity with R and are familiar with vectors, data frames, variables and using functions.

We have a crash course that covers these topics
<ul>
  <li><a target="_blank" href="https://bioinformatics-core-shared-training.github.io/r-crash-course/">R crash course</a></li>
</ul>

<p>Several Online videos are available that cover these materials. For example</p>

<ul>
<li><a target="_blank" href="http://shop.oreilly.com/product/0636920034834.do">http://shop.oreilly.com/product/0636920034834.do</a></li>
<li><a target="_blank" href="http://blog.revolutionanalytics.com/2012/12/coursera-videos.html">http://blog.revolutionanalytics.com/2012/12/coursera-videos.html</a></li>
<li><a target="_blank" href="http://bitesizebio.com/webinar/20600/beginners-introduction-to-r-statistical-software">http://bitesizebio.com/webinar/20600/beginners-introduction-to-r-statistical-software</a></li>
</ul>

<h2>
<a id="topics-covered" class="anchor" href="#topics-covered" aria-hidden="true"><span class="octicon octicon-link"></span></a>Topics Covered</h2>
<li>How R enables reproducible research </li>
<li>What constitues a tidy dataset </li>
<li>"Piping" commands together to form a workflow </li>
<li>Subseting and filtering datasets using dplyr </li>
<li>Producing summary statistics from a dataset </li>
<li>Joining datasets using dplyr </li>
<li>The grammar of graphics approach to plotting used in ggplot2 </li>
<li>Producing publication-ready graphics using ggplot2</li>

<h2>
<a id="data" class="anchor" href="#data" aria-hidden="true"><span class="octicon octicon-link"></span></a>Course Data</h2>
 Please click on this link to download all the files required to run the examples in the course:- <a href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/Course_Data.zip">CLICK HERE</a>
<br>
<h2>
<a id="software" class="anchor" href="#software" aria-hidden="true"><span class="octicon octicon-link"></span></a>Software</h2>
You will need an updated version of <a target="_blank" href="https://cran.r-project.org/">R</a> and <a target="_blank" href="https://www.rstudio.com/products/rstudio/download/">RStudio Desktop</a>.
Please check this page to make sure you have the correct versions of the software
<ul>
<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/software-check.html">Check your software install here</a></li>
</ul>
<h2>
<a id="schedule" class="anchor" href="#schedule" aria-hidden="true"><span class="octicon octicon-link"></span></a>Schedule</h2>
<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/1.introduction.html">Course Introduction</a></li>
<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/2.dplyr-intro.nb.html">Introduction to dplyr</a></li>
    <ul>
  <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/2.dplyr-intro.Rmd">Notebook</a></li>
  <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/2.dplyr-intro-exercises.Rmd">Exercise</a></li>
  <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/2.dplyr-intro-solutions.html">Solutions</a></li>
  </ul>
<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/3.workflows.nb.html">Writing analysis workflows in R</a></li>
    <ul>
   <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/3.workflows.Rmd">Notebook</a></li>
   <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/3.workflows-exercises.Rmd">Exercise</a></li>
   <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/3.workflows-solutions.html">Solutions</a></li>
    </ul>
<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/4.summarise-and-combine.nb.html">Summarising and Combining data</a></li>
    <ul>
    <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/4.summarise-and-combine.Rmd">Notebook</a></li>
    <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/4.summarise-and-combine-exercises.Rmd">Exercise</a></li>
    <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/4.summarise-and-combine-solutions.html">Solutions</a></li>
    </ul>

<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/ggplot2.html">Plotting data with ggplot2</a></li>
        <ul>
          <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/ggplot2_presentation.Rmd">Notebook</a></li>
          <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/ggplot2-exercises1-images.html">Exercises 1</a></li>
          <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/ggplot2-exercises2-images.html">Exercises 2</a></li>
          <!--<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/ggplot2-solutions1.html">Solutions 1</a></li>
          <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/ggplot2-solutions2.html">Solutions 2</a></li>-->
        </ul>
<li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/extra.html">Extra (optional) exercises on dplyr and ggplot2</a></li>
<br>
<h2>
  <a id="software" class="anchor" href="#software" aria-hidden="true"><span class="octicon octicon-link"></span></a>Software</h2>
        You will need an updated version of <a target="_blank" href="https://cran.r-project.org/">R</a> and <a target="_blank" href="https://www.rstudio.com/products/rstudio/download/">RStudio Desktop</a>.
        Please check this page to make sure you have the correct versions of the software
        <ul>
        <li><a target="_blank" href="https://rawgit.com/bioinformatics-core-shared-training/r-intermediate/master/software-check.html">Check your software install here</a></li>
        </ul>
<h2>
<a id="useful-resources" class="anchor" href="#useful-resources" aria-hidden="true"><span class="octicon octicon-link"></span></a>Useful Resources</h2>

<ul>
<li><a href="http://www.r-project.org/">The R Project for Statistical Computing</a></li>
<li><a href="https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf">The dplyr cheatsheet</a></li>
<li><a href="https://www.rstudio.com/wp-content/uploads/2015/03/ggplot2-cheatsheet.pdf">The ggplot2 cheatsheet</a></li>
<li><a href="http://vita.had.co.nz/papers/tidy-data.pdf">Hadley Wickham's Tidy Data Paper</a></li>
<li><a href="http://www.onthelambda.com/2014/02/10/how-dplyr-replaced-my-most-common-r-idioms/">Interesting blog comparing base R to dplyr</a></li>
      </section>


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