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R code / scripts

All the R code used in the labs and to make the plots in the lectures is made publicly available on a website called Github, which is popular for hosting open source software. You can navigate all the Rmd (R markdown) scripts for the labs, divided into folders by week, here:

https://github.com/genomicsclass/labs

You can download the individual Rmd scripts from Github by clicking on the week, the filename, and then the 'Raw' button.  Save this file to your computer. When saving, if your web browser tries to add a `.txt` ending, just backspace so the ending is just `.Rmd`. Then open it in RStudio. We will also put links to the Rmd scripts under the videos.

Running lab code

All software used for the class is free and open source:

  • R can be downloaded and installed from CRAN (Comprehensive R Archive Network). If possible download the latest release (R 3.0.3 released 6 March 2014).
  • We recommend using RStudio, a slick visual interface for R.
  • We will use a number of packages from Bioconductor. We will explain how to install the latest release of Bioconductor software in Week 1.