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4 changes: 1 addition & 3 deletions docs/03-data-analysts.md
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Expand Up @@ -24,7 +24,7 @@ In this guide, you will go through the following steps:

1. Create a Google account
1. [Launch Terra](https://anvil.terra.bio/#workspaces) and sign in with your Google account
1. Link external accounts (Gen3, dbGaP) to Terra (optional - enables you to import AnVIL open access datasets and to access protected data if you have appropriate authorization)
1. Link external accounts (e.g., dbGaP) to Terra (optional - enables you to import AnVIL open access datasets and to access protected data if you have appropriate authorization)

## Step 1: Create a Google Account {#data-analysts-step-1}

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The following links will take you to the Terra documentation for setting up and linking external accounts.

- [Set up a Gen3 account](https://gen3.theanvil.io/login) - allows you to use the Gen3 data explorer to create artificial cohorts over AnVIL datasets that have been indexed by Gen3.
- [Link Gen3 and Terra accounts](https://support.terra.bio/hc/en-us/articles/360050390451) - allows you to analyze Gen3 data on Terra.
- [Link Terra and eRA Commons ID](https://support.terra.bio/hc/en-us/articles/360038086332-Linking-Terra-to-External-Servers) - To use controlled-access data on Terra, you will need to link your Terra user ID to your authorization account (such as a dbGaP account). Linking to external servers will allow Terra to automatically determine if you can access controlled datasets hosted in Terra (ex. TCGA, TOPMed, etc.) based on your approved dbGaP applications.

## Wrap-Up {#data-analysts-wrap-up}
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## [13] bookdown_0.41 fastmap_1.1.1 rprojroot_2.0.4 jsonlite_1.8.8
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## [25] udpipe_0.8.11 cow_0.0.0.9000 jquerylib_0.1.4 cli_3.6.2
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Expand Up @@ -115,8 +115,8 @@ The [AnVIL Dataset Catalog](https://anvilproject.org/data) displays key NHGRI da

<img src="07-data_files/figure-html//1H5onDH7cBLK2m7fCcJ6ZodAAQ3wtJO8tNc2rwptrTPM_gf5fa6f264a_0_31.png" alt="Image shows a screenshot of the AnVIL Dataset Catalog website landing page." width="480" />

### Gen3 Data Explorer
### AnVIL Data Explorer

The [Gen3 Data Explorer and Data Commons](https://gen3.theanvil.io/) provides their API for data queries and downloads, supporting cross-project analyses. Gen3 provides access to open and protected datasets that can be exported to an AnVIL Workspace. For example, users can find the 1000 Genomes dataset on Gen3 and filter by ancestry, age, and other features prior to performing analyses on AnVIL.
The [AnVIL Data Explorer](https://explore.anvilproject.org/datasets) enables faceted searches of open and managed access datasets hosted in AnVIL, making it easier for researchers to find and custom-build cohorts.

<img src="07-data_files/figure-html//1H5onDH7cBLK2m7fCcJ6ZodAAQ3wtJO8tNc2rwptrTPM_gf5fa6f264a_0_40.png" alt="Image shows a screenshot of the Gen3 on AnVIL Data Explorer website landing page." width="480" />
<img src="07-data_files/figure-html//1H5onDH7cBLK2m7fCcJ6ZodAAQ3wtJO8tNc2rwptrTPM_g30d935bde8e_0_0.png" alt="Image shows a screenshot of the AnVIL Data Explorer website landing page." width="480" />
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Expand Up @@ -19,7 +19,7 @@ The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Spac

- The **Terra platform**: provides a compute environment with secure data and analysis sharing capabilities
- **Dockstore**: provides standards based sharing of containerized tools and workflows
- **The Gen3 data commons framework**: provides data and metadata ingest, querying, and organization
- **The AnVIL Data Explorer**: enables faceted searches of open and managed access datasets hosted in AnVIL
- **Bioconductor and Galaxy**: provide environments for users at different skill levels to construct and execute analyses

### Data Storage
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- Galaxy -- [Galaxy on AnVIL Walkthrough](https://youtube.com/watch?v=-Q4SjLEd99s) -- 5m50s 12/9/20
- Data Tables -- [Introduction to Data Tables in Terra](https://youtube.com/watch?v=IeLywroCNNA) -- 5m25s 4/5/20
- Dockstore -- [Importing a GATK workflow from Dockstore into Terra](https://youtube.com/watch?v=SGqMPNITQSE) -- 8m29s 10/15/20
- Workflows -- [Configuring and running a GATK workflow on Gen3 data in Terra](https://youtube.com/watch?v=Vr7GH_h49ts) -- 28m10s 11/25/20
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Page not found | Getting Started on AnVIL</title>
<meta name="description" content="Guides to help new AnVIL users set up their accounts and start doing research on the AnVIL platform" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />

<meta property="og:title" content="Page not found | Getting Started on AnVIL" />
<meta property="og:type" content="book" />
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<meta name="date" content="2024-10-22" />
<meta name="date" content="2024-10-28" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="9.2.1" data-path="data.html"><a href="data.html#anvil-data-library"><i class="fa fa-check"></i><b>9.2.1</b> AnVIL Data Library</a></li>
<li class="chapter" data-level="9.2.2" data-path="data.html"><a href="data.html#anvil-dataset-catalog"><i class="fa fa-check"></i><b>9.2.2</b> AnVIL Dataset Catalog</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#gen3-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> Gen3 Data Explorer</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#anvil-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> AnVIL Data Explorer</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="workflows.html"><a href="workflows.html"><i class="fa fa-check"></i><b>10</b> Workflows</a>
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## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-10-22
## date 2024-10-28
## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## bookdown 0.40 2024-07-02 [1] CRAN (R 4.3.2)
## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2)
## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0)
## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0)
## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0)
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>About the Authors | Getting Started on AnVIL</title>
<meta name="description" content="Guides to help new AnVIL users set up their accounts and start doing research on the AnVIL platform" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />

<meta property="og:title" content="About the Authors | Getting Started on AnVIL" />
<meta property="og:type" content="book" />
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<meta name="date" content="2024-10-22" />
<meta name="date" content="2024-10-28" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="9.2.1" data-path="data.html"><a href="data.html#anvil-data-library"><i class="fa fa-check"></i><b>9.2.1</b> AnVIL Data Library</a></li>
<li class="chapter" data-level="9.2.2" data-path="data.html"><a href="data.html#anvil-dataset-catalog"><i class="fa fa-check"></i><b>9.2.2</b> AnVIL Dataset Catalog</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#gen3-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> Gen3 Data Explorer</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#anvil-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> AnVIL Data Explorer</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="workflows.html"><a href="workflows.html"><i class="fa fa-check"></i><b>10</b> Workflows</a>
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## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-10-22
## date 2024-10-28
## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## bookdown 0.40 2024-07-02 [1] CRAN (R 4.3.2)
## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2)
## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0)
## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0)
## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0)
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>C Authorization Domains | Getting Started on AnVIL</title>
<meta name="description" content="Guides to help new AnVIL users set up their accounts and start doing research on the AnVIL platform" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />

<meta property="og:title" content="C Authorization Domains | Getting Started on AnVIL" />
<meta property="og:type" content="book" />
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<meta name="date" content="2024-10-22" />
<meta name="date" content="2024-10-28" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="9.2.1" data-path="data.html"><a href="data.html#anvil-data-library"><i class="fa fa-check"></i><b>9.2.1</b> AnVIL Data Library</a></li>
<li class="chapter" data-level="9.2.2" data-path="data.html"><a href="data.html#anvil-dataset-catalog"><i class="fa fa-check"></i><b>9.2.2</b> AnVIL Dataset Catalog</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#gen3-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> Gen3 Data Explorer</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#anvil-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> AnVIL Data Explorer</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="workflows.html"><a href="workflows.html"><i class="fa fa-check"></i><b>10</b> Workflows</a>
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>D Budget Templates | Getting Started on AnVIL</title>
<meta name="description" content="Guides to help new AnVIL users set up their accounts and start doing research on the AnVIL platform" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />

<meta property="og:title" content="D Budget Templates | Getting Started on AnVIL" />
<meta property="og:type" content="book" />
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<meta name="date" content="2024-10-22" />
<meta name="date" content="2024-10-28" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="9.2.1" data-path="data.html"><a href="data.html#anvil-data-library"><i class="fa fa-check"></i><b>9.2.1</b> AnVIL Data Library</a></li>
<li class="chapter" data-level="9.2.2" data-path="data.html"><a href="data.html#anvil-dataset-catalog"><i class="fa fa-check"></i><b>9.2.2</b> AnVIL Dataset Catalog</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#gen3-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> Gen3 Data Explorer</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#anvil-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> AnVIL Data Explorer</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="workflows.html"><a href="workflows.html"><i class="fa fa-check"></i><b>10</b> Workflows</a>
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Chapter 4 Consortia | Getting Started on AnVIL</title>
<meta name="description" content="Guides to help new AnVIL users set up their accounts and start doing research on the AnVIL platform" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.41 and GitBook 2.6.7" />

<meta property="og:title" content="Chapter 4 Consortia | Getting Started on AnVIL" />
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<meta name="date" content="2024-10-22" />
<meta name="date" content="2024-10-28" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="9.2.1" data-path="data.html"><a href="data.html#anvil-data-library"><i class="fa fa-check"></i><b>9.2.1</b> AnVIL Data Library</a></li>
<li class="chapter" data-level="9.2.2" data-path="data.html"><a href="data.html#anvil-dataset-catalog"><i class="fa fa-check"></i><b>9.2.2</b> AnVIL Dataset Catalog</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#gen3-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> Gen3 Data Explorer</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#anvil-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> AnVIL Data Explorer</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="workflows.html"><a href="workflows.html"><i class="fa fa-check"></i><b>10</b> Workflows</a>
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Chapter 3 Data Analysts | Getting Started on AnVIL</title>
<meta name="description" content="Guides to help new AnVIL users set up their accounts and start doing research on the AnVIL platform" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />
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<meta property="og:title" content="Chapter 3 Data Analysts | Getting Started on AnVIL" />
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<meta name="date" content="2024-10-22" />
<meta name="date" content="2024-10-28" />

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<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="9.2.1" data-path="data.html"><a href="data.html#anvil-data-library"><i class="fa fa-check"></i><b>9.2.1</b> AnVIL Data Library</a></li>
<li class="chapter" data-level="9.2.2" data-path="data.html"><a href="data.html#anvil-dataset-catalog"><i class="fa fa-check"></i><b>9.2.2</b> AnVIL Dataset Catalog</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#gen3-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> Gen3 Data Explorer</a></li>
<li class="chapter" data-level="9.2.3" data-path="data.html"><a href="data.html#anvil-data-explorer"><i class="fa fa-check"></i><b>9.2.3</b> AnVIL Data Explorer</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="workflows.html"><a href="workflows.html"><i class="fa fa-check"></i><b>10</b> Workflows</a>
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<ol style="list-style-type: decimal">
<li>Create a Google account</li>
<li><a href="https://anvil.terra.bio/#workspaces">Launch Terra</a> and sign in with your Google account</li>
<li>Link external accounts (Gen3, dbGaP) to Terra (optional - enables you to import AnVIL open access datasets and to access protected data if you have appropriate authorization)</li>
<li>Link external accounts (e.g., dbGaP) to Terra (optional - enables you to import AnVIL open access datasets and to access protected data if you have appropriate authorization)</li>
</ol>
</div>
</div>
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<p>AnVIL provides access to a wide selection of datasets, including controlled-access data. Linking your accounts will enable you to import these data into Terra.</p>
<p>The following links will take you to the Terra documentation for setting up and linking external accounts.</p>
<ul>
<li><a href="https://gen3.theanvil.io/login">Set up a Gen3 account</a> - allows you to use the Gen3 data explorer to create artificial cohorts over AnVIL datasets that have been indexed by Gen3.</li>
<li><a href="https://support.terra.bio/hc/en-us/articles/360050390451">Link Gen3 and Terra accounts</a> - allows you to analyze Gen3 data on Terra.</li>
<li><a href="https://support.terra.bio/hc/en-us/articles/360038086332-Linking-Terra-to-External-Servers">Link Terra and eRA Commons ID</a> - To use controlled-access data on Terra, you will need to link your Terra user ID to your authorization account (such as a dbGaP account). Linking to external servers will allow Terra to automatically determine if you can access controlled datasets hosted in Terra (ex. TCGA, TOPMed, etc.) based on your approved dbGaP applications.</li>
</ul>
</div>
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