live training
Bulk RNASeq: from counts to differential expression, online
Target Audience:
All VIB staff
Location:
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
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 or BioMart online
