ISB-CGC Notebooks

What’s a notebook?

Notebooks provide an interface to an interactive analysis environment. They are a mix of code (usually R or Python), descriptive explanations, and visualizations. They’re often used to demonstrate an analysis in a step by step fashion. We provide a set of notebooks below as tutorials for several frequently run analyses. You can run these through Jupyter Lab, R Studio, or Google Colaboratory.

I’m a novice, how do I…

Get started fast?	Python	R
Find GDC file locations?	Python	R
Plot a BigQuery result?	Python	R
Plot a heatmap using data in BigQuery?	Python	R
Work with cloud storage?	Python
Create cohorts of patients?	Python	R
Use PyPika or dbplyr to build a query?	Python	R
Create a complex cohort?	Python	R
Join multiple tables?	Python
Convert a .bam file to a .fastq file with samtools?	Python
Find a GA4GH Tool Repository Service (TRS) tool?	Python
Run workflow execution service (WES) tools?	Python
Use the ISB-CGC APIs?	Python	R
Explore CPTAC protein abundances?	Python
Compare protein and gene expression in CPTAC?	Python

I’m an advanced user, how do I…

Make a BigQuery table from an NCBI GEO data set?	Python
Compare cohorts with survival analysis and feature comparison?	Python	R
Run an ANOVA with BigQuery?*	Python	R
Score gene sets in BigQuery?*	Python	R
Correlate gene expression and copy number variation?	Python
Compute gene-gene expression correlation using BigQuery?	Python
Create randomized subsets of patients using BigQuery?	Python	R
Convert a 10X scRNA-seq bam file to fastq with dsub?	Python
Quantify 10X scRNA-seq gene expression with Kallisto and BUStools?	Python
Compute Nearest Centroid Classification using BigQuery?	Python	R
Use a BigQuery user defined function to perform k-means clustering?	Python
Compute correlations of protein and gene expression in CPTAC?	Python
Compare protein expression from different pipelines using CPTAC data?	Python
Calculate associations between radiomics tumor imaging features and gene expression?	Python
Analyze the correlation between gene mutations and tumor imaging features?	Python
Compare gene expression in tumor against gene expression in normal tissue?	Python
Identify cancer pathways from the Reactome database that are related to a set of genes?	Python
Integrate the Targetome and Reactome datasets to identify pathways affected by cancer drugs?	Python

*Notebook inspired by a Query of the Month Blog post

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