Background knowledge for the Tidy Transcriptomics workshop

Maria Doyle, Peter MacCallum Cancer Centre1

Stefano Mangiola, Walter and Eliza Hall Institute2

Source: vignettes/background.Rmd

Schedule

  • Part 1 Bulk RNA-seq Core
  • Part 2 Bulk RNA-seq Extended
  • Part 3 Single-cell RNA-seq

A more detailed schedule can be found here.

Format: a few introductory slides, then demos, exercises plus Q&A.
Interact: Zoom chat and polls

What is transcriptomics?

“The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells”

Wikipedia

Why use transcriptomics?

  • Genome (DNA) pretty stable
  • Proteome (proteins) harder to measure
  • Transcriptome (RNA) can measure changes in expression of thousands of coding and non-coding transcripts

Possible experimental design

How does transcriptomics work?

Types of transcriptomic analyses

  • Differential expression
  • Cell type composition
  • Alternative splicing
  • Novel transcript discovery
  • Fusions identification
  • Variant analysis

    Topics in bold we will see in this workshop

Bulk RNA sequencing differential expression workflow

Differences between bulk and single-cell RNA sequencing

Shalek and Benson, 2017

Single-cell RNA sequencing analysis workflow

Getting started

Cloud

Easiest way to run this material. Only available during workshop.
* You should have received an invite to join the classroom in the R in Pharma Organization space in RStudio Cloud.
* Login and click the “Start” button as shown in the screenshot below
* Open tidytranscriptomics.Rmd in vignettes folder

Local

If you want to install on your own computer, see instructions here. We recommend using the Cloud during the RPharma workshop and this method if you want to run the material after the workshop.

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