Bulk RNASeq: from counts to differential expression, autumn session

Bulk RNASeq: from counts to differential expression, autumn session

omics
Location:

     

Start date:

31 August 2020

Duration:

General context

The course consists of videos + a live session on counting and differential expression analysis in R and a Q&A session to answer all the questions that arise when trying the analysis on your own data 

Depending on the status of COVID19, the live sessions and the exercise sessions can be face to face or online.

Please register if you're interested in this training. One month after we reach 15 registrations the training will be organized.

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Objectives

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 

Trainers

Janick Mathys

VIB Bioinformatics Core training coordinator

Contact Janick Mathys :