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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 visualization 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 or propose 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. Introduction and setup Am I using the correct version of R for this lesson?
Why does my version of R matter?
How do I obtain the files that are used in this lesson?
00:00 2. Introduction to Bioconductor What does the Bioconductor project comprise?
How does the Bioconductor project relate to the CRAN repository?
How can I learn to use Bioconductor packages effectively?
How do I join and communicate with the Bioconductor community?
00:00 3. Installing Bioconductor packages How do I install Bioconductor packages?
How do I check if newer versions of my installed packages are available?
How do I update Bioconductor packages?
How do I find out the name of packages available from the Bioconductor repositories?
00:00 4. Getting help Where can I find help online?
Where can I ask questions to package developers and other users?
Where can I find documentation for a specific package?
Where can I learn best practices to combine multiple package into a coherent workflow?
00:00 5. S4 classes in Bioconductor What is the S4 class system?
How does Bioconductor use S4 classes?
How is the Bioconductor DataFrame different from the base data.frame?
00:00 6. Working with biological sequences What is the recommended way to represent biological sequences in Bioconductor?
What Bioconductor packages provides methods to efficiently process biological sequences?
00:00 7. Working with genomics ranges What is the recommended way to represent coordinates on a genomic scale in Bioconductor?
What Bioconductor packages provides methods to efficiently process genomic ranges?
How can I import/export sets of genomic coordinates from/to various genomic file formats?
00:00 Finish

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