Introduction to R and Bioconductor lecture

Keywords

R-programming

Authors

• Jenny Drnevich (@jenny)

Type

• Lecture

Description

This lecture gives an overview of the R and Bioconductor projects, plus the basics of R object types and programming language structure.

Aims

This lecture aims to take the novice and turn them into a beginning R user. We will describe the R environment and programming language structure so they can start to read and write code and know where to get additional help. The Bioconductor project will be described in general.

Prerequisites

• Basic computer literacy (point-and-click interface)

Target audience

Graduates students/post docs/beginning faculty with an interest in learning R, particularly for genomic data analysis. No experience with R or other programming languages are required.

Learning objectives

• Be able to describe what R is and how the programming environment works
• Be able to download and install R and add-on packages
• Be able to read, understand and write simple R code
• Appreciate how R can be used to analyze various types of scientific data, particularly genomic data using packages from Bioconductor.

Materials

• [material 1; see (instructions)[https://microasp.upsc.se/ngs_trainers/Materials/wikis/Templates#documenting-new-material] and guidelines(https://microasp.upsc.se/ngs_trainers/Materials/wikis/Git-Repos#guidelines).

Data

[Where to find the data, see our FTP solution]

Timing

4 hours (lecture: 45 min, Instructor-led exercises: 1.5 hrs, free time for swirl exercises:
1.5 hrs)

Content stability

Should be stable for any R version > 3.0

Technical requirements

• R version > 3.0
• Add-on packages: swirl, limma
• Optional: RStudio

Literature references

• Programming tools: Adventures with R
• Orchestrating high-throughput genomic analysis with Bioconductor