The ISB-CGC aims to serve the needs of a broad range of cancer researchers ranging from scientists or clinicians who prefer to use an interactive web-based application to access and explore the rich TCGA, TARGET, CCLE, COSMIC and other data sets, to computational scientists who want to write their own custom scripts using languages such as R or Python, accessing the data through APIs, and to algorithm developers who wish to spin up thousands of virtual machines to analyze hundreds of terabytes of sequence data.
The Cancer Genome Atlas project generated genomic, imaging and clinical data from thousands cancer patients. The Cancer Genomics Cloud project (ISB-CGC) aims at democratizing access to these data by providing a computational infrastructure based on the Google Cloud Platform, application programming interfaces and client-side software packages to interact with them.
The ISB-CGC team, together with Bio-IT, will provide an overview of the large scale data analysis capabilities of the platform. They will show how to query the data, fetch pre-processed data and run pan-cancer analyses within the R environment.
The ISB-CGC team, together with Bio-IT, will offer a comprehensive overview of how to use the Google Cloud Platform to process and analyse cancer data. The course will be structured into four 1.5 hours-long sessions, with the following programme:
- Day 1 – 21 June 2022, 14:00 – 15:30
- Intro to the National Cancer Institute NCI data
- Generalized intro to good clinical practices in cancer-related studies
- Q&A
- Day 2 – 22 June 2022, 14:00 – 15:30
- Introduction to SQL and R
- Exploration of NCI datasets
- Summary of days 1 and 2
- Q&A
- Day 3 – 23 June 2022, 16:00 – 17:30
- Large scale correlations in SQL
- Q&A
- Day 4 – 24 June 2022, 14:00 – 15:30
- Differential expression analysis
- Summary of days 3 and 4
- Q&A
Please note that Day 3 has a different time schedule.
Training materials
Some examples of ISB-CGC training materials and notebooks can be found here.
Bio-IT organisers and contacts
- Francesco Tabaro
- Renato Alves
- Lisanna Paladin
This course is jointly organised by Bio-IT and ISB-CGC
This course is supported by de.NBI / ELIXIR-DE
Registrations
Bookings
Bookings are closed for this event.