RaukR, Advanced R for Bioinformatics

Description

In Life Sciences and Bioinformatics, the R programming language is pivotal for data transformation, statistical analyses, and crafting publication-ready visualizations. This workshop goes beyond the basics, offering participants a comprehensive understanding of the R ecosystem. We explore best coding practices, code profiling, delve into data wrangling intricacies, emphasize reproducible research and hands-on development of web apps using R.

Course materials

Course materials will be made available at the beginning of the workshop and will remain open and publicly accessible online for at least a year. You can check out the materials from 2023.

Sessions

Our daily schedule begins with a morning session from 08:30 to 12:30, starting with breakfast from 08:30 to 09:00 and a 30-minute break at 10:30. Lunchtime is from 12:30 to 13:30. The afternoon session follows, running from 13:30 to 17:00, with a 30-minute coffee break at 15:00.

Please note that due to varying time zones, online guest lectures might occur after 17:00.

Throughout the majority of sessions, our instructors and teaching assistants will be available to aid you with practical exercises and answer any queries you may have.

Selection

We can accomodate ~42 participants. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. We do accept international applicants, but applicants affiliated to a Swedish institution are prioritized.

Once the registration period concludes, we will review your application and notify you of our decision. If accepted, you will have three working days to confirm your participation. Failure to do so would imply your inability to attend, and we will proceed accordingly. Once you confirmed, our course administrator will proceed with invoicing.

Fee

The fee for academic participants is 8000 SEK subsidized by academic grants. Fee for non-academic participants is 16 000 SEK.

Warning

If you register and are admitted but fail to attend without a valid reason (sickness or urgent family matter), you will still be liable for the entire fee.

More info about the fee

Included in the fee

• Participation in lectures and workshops
• Mingle reception with snacks and drinks
• Daily breakfast/coffee, lunch and afternoon coffee during the workshop
• One official course dinner
• Surprise social activities

Not included in the fee

• Accomodation
• Travel to and from Visby
• Daily dinners

Topics covered

• Reproducible research in R (Quarto, Rmarkdown, Renv)
• Collaborative work using Git and GitHub
• R code style guide & best practices
• Code debugging, optimization and profiling
• Parallelization and vectorization in R
• Crafting your own functions
• Object oriented programming and R classes: S3, S4, R6 and RC
• Anatomy of an R package: Creating your own package from scratch
• Tidy data flow using tidyverse
• Using the language of graphics: ggplot2
• Developing web applications using Shiny
• R and Python integration using reticulate
• Team project work - developing data analyses workflow in R using acquired skills

Pre-requisites

This workshop is aimed at both Ph.D. students and researchers within life sciences who are already using R for bioinformatics data analyses and who would like to start using R at a more advanced level. In order for you and other participants to benefit the most, you should consider yourself eligible if you are comfortable with:

• Reading and transforming data,
• Installing and using third-party packages and
• Plotting using standard R graphics.

Level

beginner