# Which tools are available?

This document introduces the tools installed in your Sandbox IVM.

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If you have questions about the tools please first search this handbook for further information. If this does not help then please contact the <finngen-servicedesk@helsinki.fi>.
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If you find a bug or would like to improve the tools then the preferred way is to create a pull request or open an issue in the tool-specific public GitHub repository.
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**Do not** include any personally identifiable (red) data in these requests. Specifically, do not take screenshots that contain red data.
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### Application menu

Many tools installed in the Sandbox are available in the **Applications menu** (see the screenshot below):

<figure><img src="/files/eAhL6pK6vqi41nhlSdjM" alt=""><figcaption></figcaption></figure>

### **Tools for cohort creation and operations**

| Tool                                                                                                | Description                                                                                            |
| --------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ |
| [Atlas](/working-in-the-sandbox/which-tools-are-available/atlas.md)                                 | Create user-defined cohorts and inspect them visually and through characterizations, export cohorts    |
| [Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co.md) | Operate cohorts made with other tools (e.g. Atlas, Genotype Browser, R), export cohorts, visualization |
| [Genotype Browser](/working-in-the-sandbox/which-tools-are-available/genotype-browser.md)           | Create cohorts based on genotype content                                                               |

### Tools for data visualization

<table><thead><tr><th width="375">Tool</th><th>Description</th></tr></thead><tbody><tr><td><a href="/pages/ydx6uVazyk8ZipXAaeE0">Trajectory Visualization Tool</a></td><td>Visualize large numbers of longitudinal cases with glyphs of user-defined conditions: Timeline viewer, Overview plots of the data, Upset plot, export cohorts &#x26; glyphs</td></tr><tr><td><a href="/pages/VJYHlLSbUjeMYUVGY6PW">Cohort Operations</a></td><td>Explore code and endpoint enrichments using CodeWAS and TimeCodeWAS, explore cohort overlaps, make overview plots of the data (upset plot)</td></tr><tr><td><a href="/pages/8ee3BeJPz7ZpmFjlvtAO">Atlas Cohort Characterizations</a></td><td>Compare two or more cohorts e.g. according to conditions, drug usage, age, sex</td></tr><tr><td><a href="/pages/MlNIN4Dc16VLYpVdGhkS">LifeTrack</a></td><td>Visualize all health register data for a person in a single view</td></tr></tbody></table>

### Tools for GWAS

| Tool                                                                                                | Description                                                                                                                                       |
| --------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
| [Custom GWAS tools](/working-in-the-sandbox/which-tools-are-available/untitled.md)                  | Tools to conduct user-defined custom GWAS                                                                                                         |
| [Pipelines](/working-in-the-sandbox/which-tools-are-available/pipelines.md)                         | Pipeline is for large-scale unmodifiable, modifiable and user-defined analysis (pipelines) with parallelization and custom sized virtual machines |
| [Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co.md) | Custom GWAS tool pipeline can be launched also from Cohort Operations                                                                             |

### Tools for genetic data browsing

| Tool                                                                                              | Description                                                                                               |
| ------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------- |
| [Genotype Browser](/working-in-the-sandbox/which-tools-are-available/genotype-browser.md)         | GenotypeBrowser is a graphical user interface to examine variant-level information within FinnGen Sandbox |
| [PGS Browser](/working-in-the-sandbox/which-tools-are-available/pgs-browser.md)                   | Browse and view polygenic scores for existing endpoints or a custom cohort                                |
| [Exome query tool](/working-in-the-sandbox/which-tools-are-available/finngen-exome-query-tool.md) | A command line interface allowing users to query carriers of variants in FinnGen exome data               |

### Other software and scripts

<table><thead><tr><th>Tool</th><th>Description</th><th data-hidden>Bug reports and improvement suggestions</th></tr></thead><tbody><tr><td><a href="/pages/c5Gm962oyYqXGGwzAc6S">Python packages</a></td><td>Python package installation instructions</td><td></td></tr><tr><td><a href="/pages/-Miuu17xF0zteZrkiGPN">R packages</a></td><td>R package installation instructions</td><td></td></tr><tr><td><a href="/pages/-Miuu17wWXdRlMkah2vB">Pre-installed Linux tools</a></td><td>Pre-installed basic (e.g. awk, grep) and FinnGen-specific Linux programs</td><td></td></tr><tr><td><a href="/pages/tDLcFb3AwSekvAO7r5Yi">Lmod linux tools</a></td><td>FinnGen-specific Linux programs loaded using Lmod</td><td></td></tr><tr><td><a href="/pages/-MhYMPpp_NWtI9l0h5zF">BigQuery</a></td><td>SQL queries</td><td></td></tr><tr><td><a href="/pages/FqF02Xk6ECiAGx9H4Q0z">Jupyter</a></td><td>Interactive coding using python language and visualization of results in notebook style</td><td></td></tr><tr><td><a href="/pages/nU8dEfYma22Rz1NGjqpy">PheWeb Users Input Validator tool</a></td><td>Validate the correct format of user-formatted input files to make custom GWAS summary stats viewable in a PheWeb-style</td><td></td></tr><tr><td><a href="/pages/vsInOU1mFQ6nVSQwvPEJ">Sandbox internal API</a></td><td>Documentation for Sandbox internal API</td><td></td></tr><tr><td><a href="/pages/MtHLcxygNw5xwPDnuH5T">Miscellaneous helper scripts/tools</a></td><td>Miscellaneous helper scripts and tools</td><td></td></tr></tbody></table>

See also a [presentation of New FinGen tools and their application to example diseases from User's meeting 28th March 2023 recording ](https://www.finngen.fi/en/members/recordings/finngen-data-users-meeting-28th-march-2023)(at 25min 23sec).


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