24-28 October 2022
Due to the COVID-19 outbreak, this course will be held online
This course aims at making Bioconductor package development within one’s reach. It is specifically designed for biologists and newer bioinformaticians who may find themselves using R/Bioconductor
packages and who wish to expand their programmatic toolkit.
Overall, this course will help the attendees gain accurate insights into the fundamental notions required for proper R/Bioconductor package development. We will cover key theory concepts about package development and the Bioconductor ecosystem, supported by a range of demonstrations and exercises, to get a complete understanding of all the steps of package development.
Throughout this workshop, we will emphasise on the best practices for developing a package embedded in the R/Bioconductor ecosystem.
The course is structured in modules over five days. Each day will contain a mix of formal lectures, demonstrations, and hands-on exercises.
Office hours will take place during the last hour of the exercises. An instructor will be available to answer individual questions related to daily exercises.
A Slack channel will also be available so that Q&A is available for everybody.
The material is suitable both for experimentalists who want to learn more about R/Bioconductor ecosystem as well as computational biologists who want to expand their set of coding skills. However, the course will be most beneficial to those who have already been familiarized with the R environment.
At the end of this course, you should be able to:
Classes are from: 2 to 8 pm Berlin time.
Introduction to package building
Local development with devtools
Introduction to Github Actions and Continuous Integration
Testing functions and pacakge
Managing dependencies & namespace
Introduction to Bioconductor: interoperability and other key notions
Creating custom Bioconductor objects
Including data to packages
Package vignettes: demonstrating how to use your package
Submitting/releasing/maintaining a Bioconductor package
Other types of Bioconductor packages: datasets, workflows, …
Disseminating your package: package support website, JOSS, rOpenSci…
Should you have any further questions, please send an email to firstname.lastname@example.org
> 30 days before the start date = 30% cancellation fee
< 30 days before the start date= No Refund.
Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.