Home

Welcome to the genVisR_workshop wiki!

Workshop title: Genomic Data Visualization and Interpretation

Topic: Advanced R and bioinformatics applications for visualization and interpretation of genomic data.

Length: 5 days (~ 9AM to 5PM with breaks)

Anticipated participants: max 30.

Target audience: Researchers and technical workers with a background in biology and a basic knowledge of linux and R

Required background: TBD

Currently this is just a list of potential topics to cover:

Table of Contents

1. Introduction 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

2. Introduction to ggplot2

   • wide vs long format
   • geom and aes
   • axis scaling and manipulation
   • faceting
   • themes and colours
   • Additional resources

3. Introduction to GenVisR

   • Waterfall plots
   • TvTi plots
   • cnSpec plots
   • cnView plots
   • lohSpec plots
   • genCov plots

4. Genome Browsers

   • IGV
   • UCSC
   • Ensembl

5. Transcript Visualization

   • ProteinPaint
   • CBioportal
   • GenVisR::lolliplot

6. Pathway Visualization

   • KEGG
   • CytoScape

7. Circos plots

8. Variant interpretation

   • CIViC