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Bioinformatics for Cancer Genomics
Workshop Pages for Students
Bioinformatics for Cancer Genomics
/site_images/CBW_cancerDNA_icon-16.jpg

Welcome

Welcome to Bioinformatics for Cancer Genomics.

The course schedule can be found here.

Pre-readings, pre-work, and laptop setup instructions can be found here here.

If you have questions or comments, visit the workshop Q&A forum. You may need to join the group by clicking on the "+" symbol and entering the class code.

You can download the printed course manual here.

Day 1

Welcome

Ann Meyer

Module 1: Introduction to Cancer Genomics

Trevor Pugh

Lecture

Module 2: Ethics of Data Usage and Security

Mark Phillips

Lecture

Module 3a: Cancer Databases

Francis Ouellette

Lecture

Module 3b: Visualization Tools

Ann Meyer

Lab lecture

Lab Practical

Logging into the Cloud

Zhibin Lu

Lab Practical: Connecting to the Cloud

Lecture

  • We have set up 27 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows (with Putty), please download this certificate.

Unix and R review

Assignment


Day 2

Module 4: Genome Alignment

Jared Simpson

Lecture

Lab Practical

Module 5: Genome Assembly

Jared Simpson

Lecture

Lab Practical

Module 6: Copy Number Variants

Sorana Morrissy

Lecture

Lab Lecture

Lab Practical

Integrative Assignment

Assignment


Day 3

Module 7: Somatic Mutations and Annotations

Sorana Morrissy

Lecture

Lab Practical

Module 8: Gene Expression

Fouad Yousif

Lecture

Ballgown code

Supplementary code

Supplementary R output

Questions with Answers PDF

Questions with Answers Word

Integrated Assignment

Integrated Assignment


Day 4

Module 9: Gene Fusion and Rearrangements

Brian Haas

Lecture

Lab Practical - CTAT Fusion Toolkit

Lab Practical - DISCASM and GMAP-Fusion

Module 10: Sharing and Scaling a VM

George Mihaiescu

Lecture

Lab practical


Day 5

Module 11: Working Reproducibly in the Cloud

Brian O'Connor

Lecture

Lab practical

Module 12: Big Data Analytics in the Cloud

Christina Yung

Lecture

Lab practical

Module 13: Genes to Pathways

Jüri Reimand

Lecture

Lab Practical - gProfiler


Day 6

Guest Lecture

Molly Hammell

Lecture

Module 14: Variants to Networks

Robin Haw

Lecture

Lab Lecture

Lab Practical

Module 9: Clinical Data Integration

Lauren Erdman

Lecture

Lab Practical

Lab Script

Data for lab part 1
Data for lab part 2