Bulk RNASeq: from counts to differential expression, online

Bulk RNASeq: from counts to differential expression, online



Start date:

23 June 2020


General context

The course consists of:

  • an online live session on counting and differential expression analysis in R on June 23rd 9h30
  • an online Q&A session to answer all the questions that arose when trying the analysis on your own data on June 30th 10h

The course will show:

  • 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

After the live session participants can analyze their own count files. Issues can be handled during the Q&A session.

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
  • Identification 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


Janick Mathys

VIB Bioinformatics Core training coordinator

Contact Janick Mathys :