Chapter 3 Software for class
Objectives:
- To familiarize ourselves with the main software used in class
- To install programs used for basic computational biology
- To perform basic tests of functionality of these programs
As I mentioned in the previous chaopter, we are going to use R, RStudio and the basic UNIX command line for our exercises, as well as atom, a basic text editor that’s widely used in programming to view and edit files.
For this course we WON’T need to install R or R studio in our computers! We will use a webpage that has R and R studio. That being said, I’ll leave this guide in case you want to install it in the future.
3.1 How to install R?
Open an internet browser and go to www.r-project.org
Click the “download R” link in the middle of the page.
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Downloading R
- Select a CRAN location (a mirror site) and click the corresponding link.
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Downloading R
- Click on the “Download R for” your operating system link at the top of the page.
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Links for R
- For Windows users: Click on the “install R for the first time” link at the top of the page. Run the
.exe
file and follow the installation instructions.
- For MacOS X users: Click on the “R-4.0.2.pkg” link to download the install package. Run the
.pkg
file and follow the installation instructions.
3.2 How to install RStudio?
- Go to www.rstudio.com and click on the “Download” link.
2. Click on “Download RStudio Desktop (FREE)” in the lower part of the page.
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Links for R
- Click on the version recommended for your system. save the .exe/.dmg file on your computer, double-click it to open, and then drag and drop it to your applications folder.
3.3 How to install Atom?
- Go to the atom webpage at https://atom.io/
- Click on Download.
- In Mac OS: Move the application to the Applications folder
- In Windows: Execute the
AtomSetup.exe
file