# 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="https://3072695768-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MhYL0UTLjqsuIdK0SSO%2Fuploads%2FhJrSyLGpkZaXIRFRykaU%2FScreenshot%202024-12-04%20at%209.34.28.png?alt=media&#x26;token=cff048ef-4a17-4fac-9594-c936d6bd6184" alt=""><figcaption></figcaption></figure>

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

| Tool                                                                                                                    | Description                                                                                            |
| ----------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ |
| [Atlas](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/atlas)                                 | Create user-defined cohorts and inspect them visually and through characterizations, export cohorts    |
| [Cohort Operations](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co) | Operate cohorts made with other tools (e.g. Atlas, Genotype Browser, R), export cohorts, visualization |
| [Genotype Browser](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/genotype-browser)           | 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="which-tools-are-available/trajectory-visualization-tool-tvt">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="which-tools-are-available/cohort-operations-tool-co">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="which-tools-are-available/atlas/detailed-guide/cohort-characterizations-in-atlas">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="which-tools-are-available/lifetrack">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](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/untitled)                  | Tools to conduct user-defined custom GWAS                                                                                                         |
| [Pipelines](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/pipelines)                         | Pipeline is for large-scale unmodifiable, modifiable and user-defined analysis (pipelines) with parallelization and custom sized virtual machines |
| [Cohort Operations](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co) | Custom GWAS tool pipeline can be launched also from Cohort Operations                                                                             |

### Tools for genetic data browsing

| Tool                                                                                                                  | Description                                                                                               |
| --------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------- |
| [Genotype Browser](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/genotype-browser)         | GenotypeBrowser is a graphical user interface to examine variant-level information within FinnGen Sandbox |
| [PGS Browser](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/pgs-browser)                   | Browse and view polygenic scores for existing endpoints or a custom cohort                                |
| [Exome query tool](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/finngen-exome-query-tool) | 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="which-tools-are-available/python-packages">Python packages</a></td><td>Python package installation instructions</td><td></td></tr><tr><td><a href="which-tools-are-available/r-libraries">R packages</a></td><td>R package installation instructions</td><td></td></tr><tr><td><a href="which-tools-are-available/unix-tools">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="which-tools-are-available/lmod-linux-tools">Lmod linux tools</a></td><td>FinnGen-specific Linux programs loaded using Lmod</td><td></td></tr><tr><td><a href="which-tools-are-available/bigquery-relational-database">BigQuery</a></td><td>SQL queries</td><td></td></tr><tr><td><a href="which-tools-are-available/bigquery-relational-database">Superset</a></td><td>Explore FinnGen data stored in BiqQuery database</td><td></td></tr><tr><td><a href="which-tools-are-available/anaconda-python-module-with-ready-set-of-scientific-packages">Jupyter</a></td><td>Interactive coding using python language and visualization of results in notebook style</td><td></td></tr><tr><td><a href="which-tools-are-available/untitled/pheweb-users-input-validator-tool">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="which-tools-are-available/sandbox-internal-api-for-software-developers">Sandbox internal API</a></td><td>Documentation for Sandbox internal API</td><td></td></tr><tr><td><a href="which-tools-are-available/miscellaneous-helper-scripts-tools">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).