Reproducible research with R: from data management to communication of results

Overview

Being able to reproduce your research results is a cornerstone of good scientific practice, not only at the level of the data generation, but also during all steps of the statistical analysis.

During this two-day workshop, we will explore how to use the R statistical software and some of the associated packages in order to conduct a reproducible data analysis and to help you reuse your R code in subsequent projects. We will cover all steps of the data analysis, starting from data cleaning and data management, going through the statistical analysis itself, and finishing with the communication of results. The content will include many tips and tricks to improve your day-to-day analysis work, making the process more efficient and robust.

In particular, we will explore "knitR" and "officeR", two R packages that allow the automated creation of documents (Word, Powerpoint, PDF, HTML, ...) from within R, thus reducing the manual steps in preparing reports or slides and increasing the reproducibility of the resulting documents. We will also discuss the use of custom-made R packages.

Audience

This course is addressed to life scientists and bioinformaticians who already routinely use the R statistical program, and would like to improve their analysis process by knowing more about R and using relevant packages.

Learning outcomes

At the end of the course, the participants are expected to be able to:

• Use R efficiently in order to perform a reproducible data analysis
• Organise their data and analysis scripts in order to make their life easier and improve the reproducibility of their work
• Avoid common traps when using R
• Directly generate reports and documents from R

Prerequisites

Knowledge / competencies

Participants should already have a basic knowledge of the R statistical software. Test your R skills with the quiz here, before registering.

Technical

Attendees should have a Wi-Fi enabled laptop, with the following software installed:

• R version > = 4.2.
• RStudio, not older than 2022.
• Attendees will need to install additional R packages during the course. Please make sure that you are able to do this (in particular from the point of view of system permissions).

Application

The registration fees for academics are 200 CHF and 1200 CHF for for-profit companies.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications will close on 01/03/2024 or as soon as the places will be filled up. Deadline for free-of-charge cancellation is set to 07/03/2024. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will take place in Zurich at the Chemistry | Biology | Pharmacy Information Center, in the ETHZ Hönggerberg campus.

The course will start at 9:00 and end around 17:00.

More information will be provided to the registered participants in due time.

Additional information

Coordination: Patricia Palagi

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.

A course delivered with the local support from: