| title | Introduction to Bioconductor |
|---|---|
| output | rmarkdown::html_vignette |
| vignette | %\VignetteIndexEntry{An Example Workshop} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} |
Authors:
Jenny Drnevich^[University of Illinois],
Ted Laderas^[Fred Hutch Cancer Center].
Last modified: 28, July 2026.
This workshop gives a quick overview of the Bioconductor project, particularly the shared infrastructure that facilitates inter-operability between Bioconductor packages. The hands-on part will explore one of the most commonly-used S4 objects, a SummarizedExperiment. We will review it's structure, how to manipulate it and make figures, and how to construct one from your own data. Finally, we will briefly explore the Bioconductor package repository and learn how to install Bioconductor on your own computer.
List any workshop prerequisites, for example:
- Basic knowledge of R syntax and RStudio
- Basic knowledge of
data.frames and how to manipulate them using thetidyverse. - Basic knowledge of Bulk RNA Sequencing (that is, you know what a count matrix is) and Experimental Design
Students will have access to a instance of RStudio / Bioconductor with runnable RMarkdown files on https://orchestraplatform.org
SummarizedExperimenttidySummarizedExperimentDESeq2
The workshop will be held in-person at Fred Hutch Cancer Center on August 10:
| Activity | Time |
|---|---|
| Exploring Bioconductor Objects | 60m |
| Loading Data into Objects | 15m |
| Installing Bioconductor and Getting Help | 15m |
- Explore and contrast how Bioconductor objects differ from
data.frames - Load your own expression count matrix and experimental metadata into an Bioconductor object.
- Install Bioconductor packages and find packages and help documentation.
Start with