Block 5: Basic R

R is a free software environment for statistical computing and graphics (R). It has become more popular in bioinformatics after the creation of Bioconductor, a serie of R packages created for biological data analysis and visualization.

This class will explain the basics about the R use such as R variables, basic operations, data loading, package usage and graph basics. As example of analysis an expression analysis will be performed during the second part of the block.

Installation Prerequisites before the Exercises:

  • R installation using Synaptic Application Manager (GUI) or apt-get install (command line). The name of the package is ‘r-base’. It’ll install 53 packages (~100 Mb). After the installation check that R is installed just typing in the terminal R --version

  • R-studio installation downloading the Debian/Ubuntu package from the R-studio web. The name of the package is: ‘RStudio 0.95.263 – Debian 6+/Ubuntu 10.04+ (32-bit)’. After the package downloading Ubuntu will open an Ubuntu Software Center page (Ubuntu 11). Check that the program has been installed opening it, it should be in Applications > Programming > RStudio. If you don’t have access to Ubuntu Software Center you can install the package in the traditional way. Move to the dir where is the package and type:
    sudo dpkg -i RStudio0.95.263-i386.deb

  • Bioconductor installation in R. Using the Terminal (Linux Terminal or R-Studio terminal), follow the instructions from the Biocounductor installation page

Presentation and Exercises Links

  • Block5_BasicR_p1_Lecture
  • Block5_BasicR_p1_Exercises
  • Block5_BasicR_p1_Solutions
  • AthKinasesGeneExpression

  • Block5_BasicR_p2_Lecture
  • Block5_BasicR_p2_Exercises
  • Block5_BasicR_p2_Solutions
  • SelectedMapKinases
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