Schedule
Schedule can be found here.
Format: Hands on demos plus Q&A Interact: Zoom chat and polls
Poll: Will you code along and/or try out exercises during this workshop?
Poll: Do you have experience with transcriptomic analyses?
Poll: Do you have experience with tidyverse?
Poll: What are you more interested in learning in this workshop?
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.
- Go to http://app.orchestra.cancerdatasci.org/1
- Launch the workshop Tidy transcriptomics for bulk and single-cell analyses shown below. It may take a minute to launch.
- Login in with the Username and Password shown.
- 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 EuroBioc2020 workshop and this method if you want to run the material after the workshop.