GitHub - sa-lee/plyrangesWorkshops (original) (raw)
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