Bulk RNASeq: from counts to differential expression

Bulk RNASeq: from counts to differential expression

advanced bioinformatics
omics
Location:

Clemenspoort, Ghent

Start date:

09 March 2020

Duration:
09 March 2020

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

VIB Bioinformatics Core training coordinator

Contact 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

Clemenspoort Gent

Overwale 3
9000 Ghent
Belgium

Public transport

09 March 2020

Clemenspoort Gent
Public transport

The train station Ghent St-Pieters is only 250 m away. We have 40 bike lots.

Route description

09 March 2020

Clemenspoort Gent
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

Clemenspoort Gent
Location contact

+32 476 46 10 40

info@clemenspoort.be