This lesson is still being designed and assembled (Pre-Alpha version)

The Bioconductor project

This lesson provides an introduction to the Bioconductor project.

A good understanding of the Bioconductor project is the foundation to efficiently use Bioconductor packages for the analysis and visulization of -omics data using R and RStudio.

We download and install R packages from Bioconductor and other repositories to write workflows and perform analyses. In order to do so, we first identify packages that are available and relevant to our analysis, and we learn from their documentation the best practices to use them as their authors intended it. For reproducibility, it is also important to identify and track versions of packages used to perform each analysis.

Sometimes, we encounter bugs in packages that we use. While it is possible to report bugs to the authors and wait for issue to be fixed, packages hosted on public repositories offer the chance to inspect the code and contribute proposed fixes ourselves. In addition to being a great opportunity to develop coding skills, community contributors are very often recognized and credited for their contributions!

In this lesson, you will learn:

Prerequisites

For Instructors

If you are teaching this lesson in a workshop, please see the Instructor notes.

Schedule

Setup Download files required for the lesson
00:00 1. Setup TODO
00:00 2. Introduction to Bioconductor What is Bioconductor?
00:00 3. Installing Bioconductor How do I install Bioconductor packages?
00:00 4. Getting help How do I access package documentation?
Where can I find help online?
Where can I ask questions to package developers and users?
00:00 5. Biostrings What is the recommended way to represent biological sequences in Bioconductor?
What packagaes and methods does Bioconductor provide to efficiently process biological sequences?
00:00 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.