R Programming for Biologists

Teaching the tools to get computers to do cool science

Creative Commons License

Computer Setup

WIS 6934 students will need their own laptops set up with R by week 2, Git by week 10, and SQL by week 13.

R

Download and install the R base system and RStudio. Both are needed. Installing RStudio will not automatically install R.

Git

Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on “Next”.
    2. Click on “Next”.
    3. Keep “Use Git from the Windows Command Prompt” selected and click on “Next”. If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on “Next”.
    5. Keep “Checkout Windows-style, commit Unix-style line endings” selected and click on “Next”.
    6. Keep “Use Windows’ default console window” selected and click on “Next”.
    7. Click on “Install”.
    8. Click on “Finish”.

Mac OS X

  1. Open up the Terminal, type in “git” and press enter.
  2. This should cause a pop-up window to appear. It will have several options; click on “Install” (not “Get Xcode”).
  3. Click “Agree”.
  4. When the install is finished, click “Done”.
  5. To make sure this worked, type in “git” in the Terminal and press enter. Some information will come up, including a list of common commands.

If this doesn’t work you can try the following:

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent “mavericks” installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled “snow-leopard” available here

Linux

Git is probably already installed. If it is not already available install it via your distro’s package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

SQL

Download and install DB Browser for SQLite

Python

Python installation is not required for WIS 6934. Python materials on this site are no longer under active development.

Download and install the Anaconda Scientific Python Distribution. I recommend you use a special editor like the Wing Intelligent Development Environment - 101.