Lab 1: Introduction to R and Bioconductor

Original Authors: Martin Morgan, Sonali Arora, Lori Shepherd
Presenting Author: Martin Morgan
Date: 20 June, 2022
Back: Monday labs

This lab has four (five!) parts. Each part consists of informative material followed by short or intermediate length exercises and case studies. The material introduces or refreshes your knowledge of R, and walks through some of the central classes and annotation resources for working with high-throughput sequence data in Bioconductor.

It’s recommended that you choose two or three of the following sections, and spend about 45 minutes to an hour on each. Take time to work through the code in the material as well as the exercises, asking questions of your colleagues and the TAs as needed. If you are relatively new to R, then consider doing sections 1 and 3. If you are new to Bioconductor, then skim the second and focus on the third and fourth sections.

Download these files:

• ALLphenoData.tsv
• BRFSS-subset.csv
• airway-sample-sheet.csv
• airway-read-counts.csv
• symgo.csv

Choose the material you’d like to cover:

1.1 Introduction to R – Gain confidence working with base R commands and data structures.

1.2 Introduction to tidy R – Gain confidence working with base R commands and data structures.

1.3 Starting an analysis – Finding R and Bioconductor packages and resources to start an analysis.

1.4 Data Representations – Learn the essentials of Bioconductor data structures

1.5 Annotation – Learn about Bioconductor resources for gene and genome annotation.