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ISB-CGC Notebooks
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What's a notebook?
------------------------

`Notebooks <https://towardsdatascience.com/jupyter-lab-evolution-of-the-jupyter-notebook-5297cacde6b>`_ 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 <https://jupyterlab.readthedocs.io/en/stable/>`_, `R Studio <https://bookdown.org/yihui/rmarkdown/notebook.html>`_, or `Google Colaboratory <https://colab.research.google.com/>`_.
  
  
I'm a novice, how do I...
-------------------------

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   * - Get started fast?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/Quick_Start_Guide_to_ISB_CGC.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/Quick_Start_Guide_to_ISB_CGC.md>`_
   * - Find GDC file locations?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_Find_GDC_File_Locations.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_Find_GDC_File_Locations.md>`_
   * - Plot a BigQuery result?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_plot_BigQuery_results.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_plot_BigQuery_results.md>`_
   * - Plot a heatmap using data in BigQuery?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_make_a_heatmap_using_BigQuery.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_make_a_heatmap_using_BigQuery.md>`_
   * - Work with cloud storage?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_work_with_cloud_storage.ipynb>`_
     - 
   * - Create cohorts of patients?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_create_cohorts.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_create_cohorts.md>`_
   * - Use PyPika or dbplyr to build a query?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_PyPika_to_create_a_BigQuery_SQL_query.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_dbplyr_to_create_a_BigQuery_SQL_query.md>`_  
   * - Create a complex cohort?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_create_a_complex_cohort.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_create_a_complex_cohort.md>`_
   * - Join multiple tables?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_complex_joins.ipynb>`_
     -
   * - Convert a .bam file to a .fastq file with samtools?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_convert_bams_to_fastq_with_samtools.ipynb>`_
     - 
   * - Find a GA4GH Tool Repository Service (TRS) tool?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_find_a_tool_using_GA4GH_TRS.ipynb>`_
     - 
   * - Run workflow execution service (WES) tools?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_a_GA4GH_tool_using_WES.ipynb>`_
     - 
   * - Use the ISB-CGC APIs?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_ISB_CGC_APIs.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_ISB-CGC_APIs.md>`_
   * - Explore CPTAC protein abundances?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_explore_CPTAC_protein_abundances.ipynb>`_
     - 
   * - Compare protein and gene expression in CPTAC?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_compare_protein_and_gene_expression_CPTAC.ipynb>`_
     - 
   * - Find data from Cancer Data Aggregator?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_cross_omics_with_CDA.ipynb>`_
     - 

I'm an advanced user, how do I...
-------------------------
  
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   :widths: 95 15 10
   :align: center
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   * - Make a BigQuery table from an NCBI GEO data set?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_make_NCBI_GEO_BigQuery_tables.ipynb>`_
     - 
   * - Compare cohorts with survival analysis and feature comparison?
     - `Python <https://nbviewer.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_quickly_compare_cohorts.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_quickly_compare_cohorts.md>`_
   * - Run an ANOVA with BigQuery?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_an_ANOVA_test_in_BigQuery.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_an_ANOVA_test_in_BigQuery.md>`_
   * - Score gene sets in BigQuery?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_score_gene_sets_with_BigQuery.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_an_ANOVA_test_in_BigQuery.md>`_
   * - Correlate gene expression and copy number variation?
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/RegulomeExplorer/Correlation_GeneExpression_vs_CNV.ipynb>`_
     - 
   * - Compute gene-gene expression correlation using BigQuery?
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/RegulomeExplorer/BigQuery-SpearmanCorrelation.ipynb>`_
     - 
   * - Create randomized subsets of patients using BigQuery?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_create_a_random_sample_in_bigquery.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_create_cohorts.md>`_
   * - Convert a 10X scRNA-seq bam file to fastq with dsub?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_10X_bamtofastq_with_dsub.ipynb>`_
     - 
   * - Quantify 10X scRNA-seq gene expression with Kallisto and BUStools?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_Kallisto_on_scRNAseq_data.ipynb>`_
     - 
   * - Compute Nearest Centroid Classification using BigQuery?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_Nearest_Centroid_Classification_with_BigQuery.ipynb>`_
     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_perform_Nearest_Centroid_Classification_with_BigQuery.md>`_
   * - Use a BigQuery user defined function to perform k-means clustering?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_cluster_data_using_a_BigQuery_function.ipynb>`_
     - 
   * - Compute correlations of protein and gene expression in CPTAC?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/RegulomeExplorer/Correlations_Protein_and_Gene_expression_CPTAC.ipynb>`_
     - 
   * - Compare protein expression from different pipelines using CPTAC data?
     - `Python <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/RegulomeExplorer/Comparing_protein_expression_from_different_pipelines_CPTAC.ipynb>`_
     -
   * - Calculate associations between radiomics tumor imaging features and gene expression?
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_compare_tumor_features_with_gene_expression_data.ipynb>`_
     -
   * - Analyze the correlation between gene mutations and tumor imaging features?
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_compare_tumor_features_with_mutation_data.ipynb>`_
     -
   * - Compare gene expression in tumor against gene expression in normal tissue?
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_analyze_differential_expression_between_paired_tumor_and_normal_samples.ipynb>`_
     - 
   * - Identify cancer pathways from the Reactome database that are related to a set of genes?
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_the_Reactome_BQ_dataset.ipynb>`_
     - 
   * - Integrate the Targetome and Reactome datasets to identify pathways affected by cancer drugs?
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/Notebooks/How_to_use_the_Targetome_and_Reactome_BQ_datasets.ipynb>`_
     -