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…¶
| How do I get started fast? | Python | R |
| How do I 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 | R |
| How do I work with cloud storage? | Python | |
| How do I create cohorts of patients? | Python | R |
| How do I use PyPika or dbplyr to build a query? | Python | R |
| How do I create a complex cohort? | Python | R |
| How do I join multiple tables? | Python | |
| How do I get started working with the COSMIC datasets? | Python | |
| 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 | |
| How do I use the ISB-CGC APIs? | Python | R |
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 quickly compare cohorts with survival analysis and feature comparison? | Python | R |
| 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 | |
| How do I do Nearest Centroid Classification using BigQuery? | Python | R |
| How do I analyze data in the COSMIC Cancer Gene Census dataset? | Python | |
| How do I use a BigQuery user defined function to cluster data using k-means clustering? | Python | |
| How do I explore CPTAC protein abundances? | Python |
*Notebook inspired by a Query of the Month Blog post