Module-01-Intro

• Introduction to Genomic Data Visualization and Interpretation

• Review of Central Concepts

• Genome Browsing and Visualization - Ensembl

• Genome Browsing and Visualization - UCSC

• Genome Browsing and Visualization - IGV

• Introduction to BioMart

• Introduction to liftover tools

• Introduction to ProteinPaint

• Introduction to COSMIC

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Module-02-R

• Using R for Genomic Data Visualization and Interpretation

• Introduction to R

• Data Munging with Data.table

• Introduction to ggplot2*

• arranging plots with ggplot2*

• ggplot2 exercises*

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Module-03-GenVisR

• Introduction to GenVisR

• Introduction to waterfall plots

• Introduction to transition/transverion plots

• Introduction to gene coverage plots

• Introduction to copy number frequency plots

• Introduction to copy number spectrum plots

• Introduction to loss of heterozygosity plots

• Introduction to sequencing coverage plots

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Module-04-Expression

• Expression Profiling, Visualization, and Interpretation

• Differential expression with DEseq2

• Pathway analysis

• Pathway visualization

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Module-05-Annotation

• Variant annotation and interpretation

• Variant annotation with VEP

• ClinVar

• CIViC

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Module-06-Review

• Q & A, Discussion, Integrated Assignments, and Working with Your Own Data

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Module-07-Appendix

• Advanced ggplot2

• Introduction to shiny

• Introduction to R Markdown