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!
How do I…¶
How do I get started fast (Python)?
How do I get started fast (R)?
How do I plot a BigQuery result (Python)?
How do I plot a BigQuery result (R)?
How do I work with cloud storage (Python)?
How do I create cohorts of patients (Python)?
How do I create cohorts of patients (R)?
How do I make an BigQuery table from an NCBI GEO data set (Python)?
How do I find a tool using the GA4GC Tool Repository Service (TRS) (Python)?
How do I convert a .bam file to a .fastq file with samtools? (Python)?
How do I convert a 10X scRNA-seq bam file to fastq with dsub? (Python)?
How do I run an ANOVA with BigQuery? (Python)?
How do I run an ANOVA with BigQuery? (R)?
How do I score gene sets in BigQuery? (Python)
How do I score gene sets in BigQuery? (R)
How do I correlate gene expression and copy number variation (Python)?
How do I compute gene-gene expression correlation using BigQuery (Python)?
What’s a 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.
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)