Introduction to Bioconductor

Authors: Jenny Drnevich1, Ted Laderas2.
Last modified: 28, July 2026.

Overview

Description

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.

Pre-requisites

List any workshop prerequisites, for example:

  • Basic knowledge of R syntax and RStudio
  • Basic knowledge of data.frames and how to manipulate them using the tidyverse.
  • Basic knowledge of Bulk RNA Sequencing (that is, you know what a count matrix is) and Experimental Design

Participation

Students will have access to a instance of RStudio / Bioconductor with runnable RMarkdown files on https://orchestraplatform.org

R / Bioconductor packages used

  • SummarizedExperiment
  • tidySummarizedExperiment
  • DESeq2

Time outline

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

Learning goals

  • 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.

Workshop

Start with

  1. University of Illinois↩︎

  2. Fred Hutch Cancer Center↩︎