live training
Bulk RNASeq: from counts to differential expression
Target Audience:
All VIB staff
Location:
General context
- R tools to generate count files like featureCounts, and summarizeOverlaps are demonstrated
- Count files from HTSeq-Count, FeatureCounts, Salmon or Kallisto are used to identify differentially expressed genes
- We START a typical functional analysis of the obtained results in order to exemplify handy tools and commercial alternatives
Participants can bring their own count files to the training.
Objectives
During this training you will:
- execute a complete workflow in R to detect differential expression
- initiate functional annotation and interpretation of the list of differentially expressed genes
Required skills
Experience in basic R programming. If you never worked in R you should attend the Basic statistics in R training first.
Software demonstrated
- Counting using Bioconductor: Rsubread - GenomicAlignments
- Identication of DE using Bioconductor: DESeq2 + other packages like tximeta (script for EdgeR is provided but not demonstrated)
- Visualization of results using R: ggplot2, pheatmap,
- Mapping of IDs to Gene symbols using Bioconductor: AnnotationDbi or BioMart online
- Functional enrichment using online tools: ToppGene, EnrichR, iRegulon...
Trainers
Janick Mathys
Program
9h30 - 13h00 Execute a complete workflow in R to detect differential expression
14h00 - 17h00 Initiate functional annotation and interpretation of the list of differentially expressed genes
Practical info
Location & Venue
09 March 2020
Ghent - Clemenspoort
Overwale 3
9000 Ghent
Belgium
Public transport
09 March 2020
Ghent - Clemenspoort
Public transport
The train station Ghent St-Pieters is only 250 m away. We have 40 bike lots.
Route description
09 March 2020
Ghent - Clemenspoort
Parking
We offer parking lots (1.20 € per hour). GPS address: Sint-Denijslaan 251.
Please take the neem the exit SPORTHAL HoGent (not Campus HoGent) and drive all the way to the end, so past the parking slots of HoGent.
Venue contact
09 March 2020
Ghent - Clemenspoort
Location contact
+32 476 46 10 40