Bioinformatics for Cancer Genomics 2017

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.

If you have questions or comments, visit the workshop Q&A forum.


Class Photo

Class Photo


Day 1

Welcome

Ann Meyer

Module 1: Introduction to Cancer Genomics

Trevor Pugh

Lecture

Recording

Module 2: Databases and Visualization Tools

Francis Ouellette

Lecture

Recording

Lab lecture

Lab Practical

Lab Practical: Connecting to the Cloud

Lecture

  • We have set up 30 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 and Winscp), please download this certificate.

Unix and R review

Assignment


Day 2

Module 3a: Genome Alignment

Jared Simpson

Lecture

Recording

Lab Practical

Module 3b: Genome Assembly

Jared Simpson

Lecture

Recording

Lab Practical

Module 4: Copy Number Variants

Sorana Morrissy

Lecture

Recording

Lab Lecture

Lab Practical


Day 3

Module 5: Somatic Mutations and Annotations

Sorana Morrissy

Lecture

Recording

Lab Lecture

Lab Practical

Module 6: Gene Expression

Fouad Yousif

Lecture

Recording

Lab Practical

Ballgown code

Supplementary code

Integrated Assignment

Integrated Assignment


Day 4

Module 7: Gene Fusion and Rearrangements

Andrew McPherson

Lecture

Recording

Rearrangements

Lab Practical

Gene Fusions

Lab Practical - Installation

Lab Practical - Prediction

Lab Practical - Exploration

Lab Practical - Visualization

Module 8: Variants to Networks

Juri Reimand

Lecture a

Recording

Lecture b

Recording

Lab Practical - Annovar

Lab Practical - gProfiler


Day 5

Module 8: Variants to Networks

Lincoln Stein and Robin Haw

Lecture

Recording

Lab Lecture

Lab Practical

Guest Lecture

Steve Jones

Lecture

Module 9: Clinical Data Integration

Anna Goldenberg

Lecture

Recording

Lab Practical

Lab Script

Data for lab part 1
Data for lab part 2


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