Bioinformatics for Cancer Genomics 2019
Welcome
Welcome to Bioinformatics for Cancer Genomics 2019.
The course schedule can be found here.
Meet your faculty here
CLASS MATERIALS: You can download the printed course manual here.
Lecture 1 from Trevor
Lecture 3 from Francis
Pre-Workshop Materials
Laptop Setup Instructions
Instructions to setup your laptop can be found here.
Pre-workshop Tutorials
Pre-readings and pre-work can be found here here.
It is in your best interest to complete these before the workshop.
Class Photo
Day 1
Welcome
Michelle Brazas
Module 1: Introduction to Cancer Genomics
Trevor Pugh
Module 2: Ethics of Data Usage and Security
Mark Phillips
Module 3: Databases and Visualization Tools
Francis Ouellette
Module 3 Lab: IGV
Heather Gibling
Logging into the Cloud
Zhibin Lu
Lab Practical: Connecting to the Cloud
- We have set up 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 CBWCG.pem from Slack; Otherwise if you plan on using Windows (with Putty), please download CBWCG.ppk from Slack.
Mac Key
Windows Key
Unix and R review
Heather Gibling
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 6 Lab
Sorana Morrissy
Module 7: Somatic Mutations and Annotations
Sorana Morrissy
Lecture
Lecture in PPT
Updated Lecture
Module 8: Gene Expression Profiling
Florence Cavalli
Integrative Assignment
Day 4
Module 8 Lab
Florence Cavalli
Module 9: Gene Fusion and Rearrangements
Brian Haas
Lab Practical - CTAT Fusion Toolkit
Lab Practical - DISCASM and GMAP-Fusion
Module 10: Genes to Pathways
Jüri Reimand
Data Sets - Genelist_GBM.txt
Data Sets - Genelist_KIRC.txt
Data Sets - hsapiens.pathways.NAME.gmt
Day 5
Module 11: Variants to Networks
Robin Haw
Module 12: Integration of Clinical Data
Lauren Erdman
Data for lab part 1
Data for lab part 2
Post Workshop
Post workshop content for data sets, docker containers, AWS image, tools and install instructions can be found here
Thank you for attending the Bioinformatics for Cancer Genomics workshop! Help us make this workshop better by filling out our survey.