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 | |
| Get started working with the COSMIC datasets? | 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 |
| Analyze data in the COSMIC Cancer Gene Census dataset? | Python | |
| 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 |
*Notebook inspired by a Query of the Month Blog post