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.
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 plot a heatmap using data in BigQuery? Python
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 find a tool using the GA4GH Tool Repository Service (TRS)? Python
How do I run a tool using a workflow execution service (WES)? 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 create randomized subsets of patients using BigQuery? Python / R
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)