Institute of Molecular Genetics

Oct 8 - 9, 2016

9:00 am - 5:00 pm

Instructors: Nasťa Zidkova, Filip Sedlák, Petr Šimeček, Libor Mořkovský

Helpers: Václav Gergelits, Vojtěch Filipec, Petr Švarný, Michal Kahle

General Information

This course will help you to use the computer more efficiently during your research. We'll show you how to automate repetitive procedures like manipulating files, computing statistics and creating charts from your data. This will help you make your analyses less error prone and reproducible.

If you're eager to learn but you don't see the use of such skills in your research, don't worry. The more you know, the more cases you'll see where you can apply your newly acquired skills.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Vídeňská 1083, Prague. Get directions with

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Price: This course is offered to you at courtesy of the instructors and helpers. Please smile at them. :-) There is no budget for food and beverages. If you'd like to return the favour, you're more than welcome to bring in any meal or snack.

Contact: Please mail for more information.

Registration is closed now :-( See you next time!


Don't take the schedule too seriously, it may change.

Day 1

09:00 Introductions
  • Introduction to RStudio
  • Using R as calculator
  • Reading files, using data.frame
  • Variables, data types
  • Functions
12:00 Lunch break
  • Functions (continued)
  • Subsetting
  • Conditions and loops
  • Base graphics
  • Plotting wiht ggplot2
17:00 Wrap-up

Day 2

  • Writing data — files, images
  • Using apply, lapply instead of loops
  • Transforming data with dplyr and tidyr
12:00 Lunch break
16:00 Wrap-up

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Course material and further reading

Programming with R

Basic Software Carpentry course teaching R programming.

R for Reproducible Scientific Analysis

R course focused on manipulating data.

Data Carpentry Genomics workshop

Course from Data Carpentry teaching how to analyze genomics data using R and commandline tools.

Day 1

Introduction to RStudio, using R as a calculator

Lecture 1, Lecture 2

Reading files, using data frames

Lecture 1, Lecture 2

Variables, data types



Lecture 1, Lecture 2



Conditions, loops

Lecture 1, Lecture 2, Lecture 3

Base graphics




Day 2

Writing files, saving pictures


Apply, lapply






R markdown


Introduction to bioconductor


Best practices in R



To participate in a Software for Scientists workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

R Studio

R Studio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Can’t I just use R?

RStudio makes R easier to use. We'll teach the course using R Studio.

Download and installation

  1. Install R. Download package for your system at CRAN. Then run the installer.
    • Linux only - you may already have R in your package manager. In Ubuntu, you can run sudo apt-get install r-recommended
  2. Install R Studio. Download package for your system at RStudio Desktop download and run the installer.

Video tutorial

Video by