Session content

Classes from 09:30 to 17:30

 Lecture 1 –Introduction to Genomic Data Visualization and Interpretation

 

  • Central dogma

  • Omic technologies and data

  • Reference files: GTF, BAM, VCF, MAF, BED, etc

  • Genome annotation resources, browsers, etc.

  • Introduction to demonstration data sets



Lab 1 – Genome Browsing and Visualization exercises

 

  • IGV

    • Basics

    • Creating custom genomes

    • Sashimi plots

  • UCSC

  • Ensembl

 

Lab 2 –Web resources for variant annotation and visualization

 

  • VEP/SnpEff

  • ProteinPaint

  • CBioportal

  • Ensembl BioMart

 

 

Classes from 09:30 to 17:30

Lecture 2 –  Introduction to R for Genomic Data Visualization and Interpretation

 

Lab 3 – Intro to R

 

  • Installation

  • CRAN and Bioconductor

  • Data types

  • Reading and writing Data

  • Data Frames, slicing, and manipulation

  • Basic control structures

  • apply() family of functions

  • Additional resources

 

Lab 4 – Intro to ggplot

 

  • wide vs long format

  • geom and aes

  • axis scaling and manipulation

  • faceting

  • themes and colours

  • ggvis

  • Additional resources

 

Lab 5 –Real world examples using ggplot

 

  • Heatmaps

  • Regression lines

  • Survival analysis

  • circos

 

Classes from 09:30 to 17:30

Lab 6 –Popular genomic visualizations with GenVisR

 

  • Waterfall plots

  • TvTi plots

  • cnSpec plots

  • cnView plots

  • lohSpec plots

  • genCov plots

 

Lecture 3 –Differential gene expression and pathway analysis

 

Lab 7 –Differential expression analysis

  • DEseq2

 

Classes from 09:30 to 17:30

 Lab 8 –Tools and datasets for pathway analysis

 

  • KEGG

  • GO

  • GAGE (R package)

 

Lab 9 – Pathway visualization

 

  • Pathview (R package)

  • Cytoscape

 

Lecture 4 – Pathway visualization

 

Lab 10  – Clinical variant interpretations

 

  • Variant identity

    • HGVS

    • TransVar

    • Mutalyzer

 

  • ClinVar

  • CIViC

 

 

Classes from 09:30 to 17:30

Lecture 5 - Review. Question and Answer. Open discussion.

 

Lab 11a- Optional integrated exercises


Lab 11b- Customized visualization and interpretation of your own data