Bioinformatics for Cancer Genomics
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.
Class Photo
Day 1
Welcome
Ann Meyer
Module 1: Introduction to Cancer Genomics
Trevor Pugh
Module 2: Ethics of Data Usage and Security
Mark Phillips
Module 3a: Cancer Databases
Francis Ouellette
Module 3b: Visualization Tools
Ann Meyer
Logging into the Cloud
Zhibin Lu
Lab Practical: Connecting to the Cloud
- 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
Day 2
Module 4: Genome Alignment
Jared Simpson
Module 5: Genome Assembly
Jared Simpson
Module 6: Copy Number Variants
Sorana Morrissy
Integrative Assignment
Day 3
Module 7: Somatic Mutations and Annotations
Sorana Morrissy
Module 8: Gene Expression
Fouad Yousif
Integrated Assignment
Day 4
Module 9: Gene Fusion and Rearrangements
Brian Haas
Lab Practical - CTAT Fusion Toolkit
Lab Practical - DISCASM and GMAP-Fusion
Module 10: Sharing and Scaling a VM
George Mihaiescu
Integrated Assignment
Day 5
Module 11: Working Reproducibly in the Cloud
Brian O'Connor
Module 12: Big Data Analytics in the Cloud
Christina Yung
Module 13: Genes to Pathways
Jüri Reimand
Day 6
Guest Lecture
Molly Hammell
Module 14: Variants to Networks
Robin Haw
Module 15: Clinical Data Integration
Lauren Erdman
Data for lab part 1
Data for lab part 2
Recap
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