Community Notebooks

Welcome to our collection notebooks, demonstrating the powerful combination of BigData from the NCI cancer programs (like TCGA), and powerful cloud-based tools from Google.

Please let us know if you have suggestions, ideas, or thoughts for a notebook example!

What’s a Jupyter notebook?

Notebooks are documents that mix code (usually R or python), descriptive explainations, and visualizations. They’re ideal for explaining an analysis. Also idea for tutorials because of the ‘hands on’ nature.

Jupyter notebooks

Jupyter lab notebooks

How to use a python notebook.

How to use an R notebook.

How do I…

How do I quantify 10X scRNA-seq gene expression with Kallisto and BUStools? (Python)?


Provided by the ISB-CGC team, featuring special efforts by:

  • Lauren Hagen (lauren.hagen ( ~ at ~ ) systemsbiology ( ~ dot ~ ) org)
  • Kawther Abdilleh (kawther.abdilleh ( ~ at ~ ) gdit (~ dot ~) com)
  • John Cornelius (john.cornelius ( ~ at ~ ) systemsbiology ( ~ dot ~ ) org)
  • David L Gibbs david.gibbs ( ~ at ~ ) systemsbiology ( ~ dot ~ ) org)
  • Sheila M Reynolds (sheila.reynolds ( ~ at ~ ) systemsbiology ( ~ dot ~ ) org)

Have feedback or corrections? Please email us at feedback@isb-cgc.org.