**************************
Quick Links 
**************************

The table below describes the types of functions that can be performed in ISB-CGC and provides links to documentation on how to do those functions.

+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|Function                               |In GUI                                                                                                                                                                                                                                                                                       |With Command Line                                                                                                                                                                                                                                                                                |
+=======================================+=============================================================================================================================================================================================================================================================================================+=================================================================================================================================================================================================================================================================================================+
|**Work on the Google Cloud Platform**  |- `Link to the Google Cloud Platform Console <https://console.cloud.google.com/>`_                                                                                                                                                                                                           |- `Google Cloud SDK <https://cloud.google.com/sdk/>`_                                                                                                                                                                                                                                            |
|                                       |- Getting a trial account on the Google Cloud Platform `sponsored by Google <https://console.developers.google.com/billing/freetrial>`_                                                                                                                                                      |- `Google Cloud Shell <https://cloud.google.com/shell/docs/>`_                                                                                                                                                                                                                                   |
|                                       |- Getting a trial account on the Google Cloud Platform `sponsored by ISB-CGC <Support.html#request-gcp>`_                                                                                                                                                                                    |- `Authenticating with Google <gcp-info/gcp-info2/Setup.html#authenticategoogle>`_ (two approaches: `gcloud init <https://cloud.google.com/sdk/gcloud/reference/init>`_ and/or `gcloud auth login <https://cloud.google.com/sdk/gcloud/reference/auth/login>`_)                                  |
|                                       |- General information on how to use the `Google Cloud Platform Console <https://support.google.com/cloud/?hl=en#topic=3340599>`_                                                                                                                                                             |                                                                                                                                                                                                                                                                                                 |
|                                       |- `Specific information <gcp-info/gcp-info2/Setup.html>`_ on how to set up your GCP project for use with ISB-CGC                                                                                                                                                                             |                                                                                                                                                                                                                                                                                                 |
|                                       |- How to `manage project members and change member permissions <https://support.google.com/cloud/answer/6158846>`_                                                                                                                                                                           |                                                                                                                                                                                                                                                                                                 |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Explore what data are available**    |- `Documentation <Hosted-Data.html>`_                                                                                                                                                                                                                                                        |- BigQuery `R and Python Tutorials <progapi/Tutorials.html>`_                                                                                                                                                                                                                                    |
|                                       |- `GUI <webapp/Saved-Cohorts.html>`_                                                                                                                                                                                                                                                         |- `ISB-CGC Endpoints <progapi/Programmatic-API.html>`_                                                                                                                                                                                                                                           |
|                                       |                                                                                                                                                                                                                                                                                             |- `Google Genomics APIs <data/data2/data_in_GG.html>`__                                                                                                                                                                                                                                          |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Understand details of the data**     |- `Access controlled data <webapp/Gaining-Access-To-Contolled-Access-Data.html>`_                                                                                                                                                                                                            |- For data in BigQuery                                                                                                                                                                                                                                                                           |
|                                       |- `View File List <webapp/Saved-Cohorts.html#viewfilelist>`_ in GUI                                                                                                                                                                                                                          | - BigQuery `Command Line Tool <https://cloud.google.com/bigquery/bq-command-line-tool-quickstart>`_                                                                                                                                                                                             |
|                                       |- `View Sequences with IGV <webapp/IGV-Browser.html>`_                                                                                                                                                                                                                                       | - BigQuery `REST API <https://cloud.google.com/bigquery/bigquery-api-quickstart>`_                                                                                                                                                                                                              |
|                                       |- `Google BigQuery Web UI <progapi/bigqueryGUI/WalkthroughOfGoogleBigQuery.html>`_                                                                                                                                                                                                           |- For data in Google Cloud Storage                                                                                                                                                                                                                                                               |
|                                       |- `Google API Explorer <https://apis-explorer.appspot.com/apis-explorer/?base=https://api-dot-isb-cgc.appspot.com/_ah/api#p/>`_                                                                                                                                                              | - Google `Cloud Storage JSON API <https://cloud.google.com/storage/docs/json_api/>`_                                                                                                                                                                                                            |
|                                       |                                                                                                                                                                                                                                                                                             | - Google Cloud Storage `gsutil <https://cloud.google.com/storage/docs/gsutil>`_                                                                                                                                                                                                                 |
|                                       |                                                                                                                                                                                                                                                                                             |- For data in Google Genomics                                                                                                                                                                                                                                                                    |
|                                       |                                                                                                                                                                                                                                                                                             | - `Google Genomics REST API <https://cloud.google.com/genomics/reference/rest/>`_                                                                                                                                                                                                               |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Analyze ISB-CGC data**               |- `Analyses <webapp/Workbooks.html>`_ with Bar Charts, Histograms, Scatter Plots, Violin Plots, Cubby Hole Plots and SeqPeek                                                                                                                                                                 |- BigQuery `R and Python Tutorials <progapi/Tutorials.html>`_                                                                                                                                                                                                                                    |
|                                       |- `Google BigQuery Web UI <progapi/bigqueryGUI/WalkthroughOfGoogleBigQuery.html>`_  and `BigQuery UI Walkthrough <https://raw.githubusercontent.com/isb-cgc/readthedocs/master/docs/include/intro_to_BigQuery.pdf>`__                                                                        |- ISB-CGC `Endpoints <progapi/Programmatic-API.html>`_                                                                                                                                                                                                                                           |
|                                       |                                                                                                                                                                                                                                                                                             |- `Google Genomics APIs <data/data2/data_in_GG.html>`__                                                                                                                                                                                                                                          |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Create cohorts of patients**         |- `Create cohorts <webapp/Saved-Cohorts.html>`_                                                                                                                                                                                                                                              |- Use GUI saved cohorts in ISB-CGC `Endpoints <progapi/Programmatic-API.html>`_                                                                                                                                                                                                                  |
|                                       |- Cohorts `set operations <webapp/Saved-Cohorts.html#set-operations>`_                                                                                                                                                                                                                       |- de novo using ISB-CGC `Endpoints <progapi/Programmatic-API.html>`_, BigQuery `Command Line Tool <https://cloud.google.com/bigquery/bq-command-line-tool-quickstart>`_, and/or BigQuery `REST API <https://cloud.google.com/bigquery/bigquery-api-quickstart>`_                                 |
|                                       |- Create a cohort from visualization (`background <webapp/Saved-Cohorts.html#creating-a-cohort-from-a-visualization>`_ and `tool image <webapp/Workbooks.html#selectionicon>`_)                                                                                                              |                                                                                                                                                                                                                                                                                                 |
|                                       |- Develop queries with `Google BigQuery Web UI <progapi/bigqueryGUI/WalkthroughOfGoogleBigQuery.html>`_ and/or `Google API Explorer <https://apis-explorer.appspot.com/apis-explorer/?base=https://api-dot-isb-cgc.appspot.com/_ah/api#p/>`_ before creating cohorts with command line tools |                                                                                                                                                                                                                                                                                                 |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Add your data to the cloud**         |- Uploading your low level data (e.g. Bam and VCF files) to `Google Cloud Storage <webapp/program_data_upload.html#low-level-files-for-api-access>`_                                                                                                                                         |- Uploading your data to Google `Cloud Storage <https://cloud.google.com/storage/docs/cloud-console#_using>`_                                                                                                                                                                                    |
|                                       |- `Upload high level summary data <webapp/program_data_upload.html>`_ (such as Methylation, Gene Expression, microRNA, Protein Expression & Customized data) for plotting in the UI.                                                                                                         |- Uploading your data to Google `BigQuery <https://cloud.google.com/bigquery/loading-data-into-bigquery>`_                                                                                                                                                                                       |
|                                       |                                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                                                 |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Analyze your data with ISB-CGC data**|- `Plot your high level experimental data <webapp/GraphingUserData.html>`_ (such as Methylation, Gene Expression, microRNA, Protein Expression and Customized data) with other ISB-CGC data (e.g. TCGA).                                                                                     |- BigQuery `R and Python Tutorials <progapi/Tutorials.html>`_                                                                                                                                                                                                                                    |
|                                       |                                                                                                                                                                                                                                                                                             |- ISB-CGC `Endpoints <progapi/Programmatic-API.html>`_                                                                                                                                                                                                                                           |
|                                       |                                                                                                                                                                                                                                                                                             |- `Google Genomics APIs <data/data2/data_in_GG.html>`__                                                                                                                                                                                                                                          |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Run bioinformatics pipelines/tools** |                                                                                                                                                                                                                                                                                             |- Google Compute Engine `getting started guide <progapi/Compute-Engine.html>`_                                                                                                                                                                                                                   |
|                                       |                                                                                                                                                                                                                                                                                             |- `Compute examples in Github <https://github.com/isb-cgc/examples-Compute>`_ (with Common Workflow Language (CWL) and grid examples)                                                                                                                                                            |
|                                       |                                                                                                                                                                                                                                                                                             |- `Useful recipes <https://googlegenomics.readthedocs.org/en/latest/sections/process_data.html>`_ in the `Google Genomics Cookbook <https://googlegenomics.readthedocs.org/en/latest/index.html>`_                                                                                               |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|**Import Genomic Data Commons lists**  |                                                                                                                                                                                                                                                                                             |- `Introduction <GDCTutorials/FromGDCtoISBCGC.html>`_                                                                                                                                                                                                                                            |
|                                       |                                                                                                                                                                                                                                                                                             |- `Importing GDC File Manifests <GDCTutorials/ImportGDCFileManifest.html>`_                                                                                                                                                                                                                      |
|                                       |                                                                                                                                                                                                                                                                                             |- `Importing GDC Case lists <GDCTutorials/ImportGDCCaseDownload.html>`_                                                                                                                                                                                                                          |
+---------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+