Bulk RNASeq: from counts to differential expression
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.
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
Experience in basic R programming. If you never worked in R you should attend the Basic statistics in R training first.
- 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
Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases.
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
09 March 2020
Ghent - Clemenspoort
Overwale 3
9000 Ghent
Belgium
09 March 2020
Ghent - Clemenspoort
The Clemenspoort, the Clemenshuis, and the Clemenshof are integrated into a network of other buildings on the grounds of the former Redemptorist monastery, now the Overwale street.
Located just 250 meters from Ghent St. Pieters Station.
09 March 2020
Ghent - Clemenspoort
40 bike parking lots available.
09 March 2020
Ghent - Clemenspoort
Parking facilities available (€ 1.80 per hour). GPS address: Sint-Denijslaan 251. Take the driveway of the HoGent Sports Hall (not the HoGent Campus) and drive all the way to the end - past the HoGent parking areas. If you are registered in the 411 app, activate your license plate under the option 'Garage parking via license plate'. The barrier will open automatically, and payment will be processed via 4411.
09 March 2020
Ghent - Clemenspoort
+32 476 46 10 40