Fluent genomic data analysis with plyranges

Instructor(s) name(s) and contact information

Stuart Lee - lee.s at wehi.edu.au

Michael Lawrence - lawremi at gmail

Workshop Description

In this workshop, we will give an overview of how to perform low-level analyses of genomic data using the grammar of genomic data transformation defined in the plyranges package. We will cover:

• introduction to GRanges
• overview of the core verbs for arithmetic, restriction, and aggregation of GRanges objects
• performing joins between GRanges objects
• using the above to perform coverage analysis

The workshop will be a computer lab, in which the participants will be able to ask questions and interact with the instructors.

Pre-requisites

This workshop is mostly self-contained however familiarity with the following would be useful:

• plyranges vignette
• the GenomicRanges and IRanges packages
• tidyverse approaches to data analysis

Workshop Participation

Students will work through an Rmarkdown document while the instructors respond to any questions they have.

R / Bioconductor packages used

• plyranges
• HelloRanges

Time outline

Activity	Time
Introduction and plan	10m
Basic wrangling	20m
Coverage analysis	20m

Workshop goals and objectives

Learning goals

• Understand that GRanges follows tidy data principles
• Apply the plyranges grammar to genomic data analysis

Learning objectives

• Read files into R as GRanges objects
• Perform coverage analysis
• Build data pipelines for analysis based on GRanges