6-14 May 2020
Zoom
Europe/Berlin timezone

Registration deadline: 16 April 2020

Course aim: Research in the field of biology now often involves the acquisition of large datasets.  In order to get the most out of such large and complex datasets it is useful to know how to efficiently structure such data and the methods available to manipulate and visualize large datasets.  This course is aimed at those with limited or no programming experience and aims to teach participants the basics of data analysis and visualization using the R statistical programming language.

Learning Outcomes: This course will enable students to get started with data analysis using R. Topics covered include, importing data into R, formatting data for easy further analysis, manipulating tabular data and performing basic calculations, creating publication quality figures, and creating complete data analysis reports.

The number of participants is limited to 20.  The course is open for DIPP PhD students and CBG Postdocs.

We will inform you after 17 April 2020 whether a slot in the programming course could be assigned to you!

 

 

 

Starts
Ends
Europe/Berlin
Zoom
 

Lecturers: Lena Hersemann, Antonio Domingues & Ian Henry - MPI-CBG Scientific Computing Facility

Course Structure: The course will include presentations to introduce important topics, live coding sessions where the instructor and students write code together, and exercises for students to work on individually or in small groups.  The course is intended to be very hands on with plenty of opportunity for students to ask questions. 

Topics covered include:

  • Importing data into R (e.g. from Excel)
  • Formatting data for easy further analysis
  • Manipulating tabular data and performing basic calculations
  • Creating publication quality plots
  • Creating complete analysis reports
 
 
Day 1 (May 6) 9.00-13.00:
Introduction (Rstudio fundamentals, R basics), importing data into R
 
Day 2 (May 7) 9.00-13.00:
Data manipulation (dplyr)
 
Day 3 (May 8) 9.00-13.00:
Data plotting (ggplot2)
 
Day 4 (May 13) 9.00-13.00:
Data reshaping (tidyr)
 
Day 5 (May 14) 9.00-13.00:
Generating data analysis reports (RMarkdown)
 

How to prepare your computer before the course

Installing Software

In order to take part in this course you should install the following software on your computer.

Additional Notes:

MacOSX: Installation of the above software may require you to over-ride the default security settings on your Mac as it may complain that the software is from an untrusted source.  This can be temporarily done by right-clicking the downloaded installation file icon and then clicking open rather than double clicking the icon.

Installing R Packages

We would also like to ask you to check you have the required R packages for the course.  To simplify this procedure we would ask you to open RStudio (installed above) and run the following command from the R console window within RStudio (just copy and paste the 2 lines below and press the "enter key" sometimes marked "<-|" or "return").

if (!require("devtools")) install.packages("devtools")  
devtools::source_url("https://git.mpi-cbg.de/snippets/21/raw")

Note: It may take 5-10 minutes to complete installation and will require a reliable internet connection for installation. If you lose connection in the middle of the install then you can always re-run the two lines above.

You should get a message saying everything worked fine as well as the password required for the Zoom meetings.  If you don't get this message, then please send an email to bioinformatics@mpi-cbg.de and we will arrange a short meeting so that we can prepare your laptop for the course and inform you about the password.

If the output contains the following message you are ready for the course (you may also get additional red warning/information messages but these can largely be ignored for the time being).

###
###
### Your R is ready for the SciComp R-Course!
###
### Password: ******

###
###

Additional Notes:

Linux: The installation of the devtools package depends on the curl R package which in-turn requires libcurl-devel to be present otherwise the install.packages call will produce an error and quit.  Should you have any problems installing the software under Linux, please let us know.

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