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.

I’m a novice, how do I…

How do I get started fast? Python / R

How to find GDC file locations? Python / R

How do I plot a BigQuery result? Python / R

How do I work with cloud storage? Python

How do I create cohorts of patients? Python / R

How do I create a complex cohort? Python / R

How do I convert a .bam file to a .fastq file with samtools? Python

How do I use the GA4GH Tool Repository Service (TRS)? Python

I’m an advanced user, how do I…

How do I make a BigQuery table from an NCBI GEO data set? Python

How do I run an ANOVA with BigQuery? Python / R

How do I score gene sets in BigQuery? Python / R

How do I correlate gene expression and copy number variation? Python

How do I compute gene-gene expression correlation using BigQuery? Python

How do I convert a 10X scRNA-seq bam file to fastq with dsub? Python

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


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

  • Kawther Abdilleh (kawther.abdilleh ( ~ at ~ ) gdit (~ dot ~) com)
  • Boris Aguilar (boris.aguilar ( ~ at ~ ) systemsbiology ( ~ dot ~ ) org)
  • Lauren Hagen (lauren.hagen ( ~ at ~ ) systemsbiology ( ~ dot ~ ) org)
  • David L Gibbs (david.gibbs ( ~ at ~ ) systemsbiology ( ~ dot ~ ) org)
  • Fabian Seidl (fabian.seidl ( ~ at ~ ) gdit ( ~ dot ~ ) com)
  • Ronald Taylor (ronald.taylor1 ( ~ at ~ ) gdit ( ~ dot ~ ) com)

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