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? |
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Find GDC file locations? |
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Plot a BigQuery result? |
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Plot a heatmap using data in BigQuery? |
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Work with cloud storage? |
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Create cohorts of patients? |
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Use PyPika or dbplyr to build a query? |
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Create a complex cohort? |
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Join multiple tables? |
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Get started working with the COSMIC datasets? |
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Convert a .bam file to a .fastq file with samtools? |
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Find a GA4GH Tool Repository Service (TRS) tool? |
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Run workflow execution service (WES) tools? |
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Use the ISB-CGC APIs? |
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Explore CPTAC protein abundances? |
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Compare protein and gene expression in CPTAC? |
I’m an advanced user, how do I…¶
Make a BigQuery table from an NCBI GEO data set? |
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Compare cohorts with survival analysis and feature comparison? |
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Run an ANOVA with BigQuery?* |
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Score gene sets in BigQuery?* |
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Correlate gene expression and copy number variation? |
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Compute gene-gene expression correlation using BigQuery? |
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Create randomized subsets of patients using BigQuery? |
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Convert a 10X scRNA-seq bam file to fastq with dsub? |
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Quantify 10X scRNA-seq gene expression with Kallisto and BUStools? |
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Compute Nearest Centroid Classification using BigQuery? |
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Analyze data in the COSMIC Cancer Gene Census dataset? |
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Use a BigQuery user defined function to perform k-means clustering? |
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Compute correlations of protein and gene expression in CPTAC? |
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Compare protein expression from different pipelines using CPTAC data? |
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Calculate associations between radiomics tumor imaging features and gene expression? |
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Analyze the correlation between gene mutations and tumor imaging features? |
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Compare gene expression in tumor against gene expression in normal tissue? |
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Identify cancer pathways from the Reactome database that are related to a set of genes? |
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Integrate the Targetome and Reactome datasets to identify pathways affected by cancer drugs? |
*Notebook inspired by a Query of the Month Blog post