Which tools are available?

This document introduces the tools installed in your Sandbox IVM.

If you have questions about the tools please first search this handbook for further information. If this does not help then please contact the [email protected].

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.

Do not include any personally identifiable (red) data in these requests. Specifically, do not take screenshots that contain red data.

Application menu

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

Tools for cohort creation and operations

Tool	Description
Atlas	Create user-defined cohorts and inspect them visually and through characterizations, export cohorts
Cohort Operations	Operate cohorts made with other tools (e.g. Atlas, Genotype Browser, R), export cohorts, visualization
Genotype Browser	Create cohorts based on genotype content

Tools for data visualization

Tool	Description
Trajectory Visualization Tool	Visualize large numbers of longitudinal cases with glyphs of user-defined conditions: Timeline viewer, Overview plots of the data, Upset plot, export cohorts & glyphs
Cohort Operations	Explore code and endpoint enrichments using CodeWAS and TimeCodeWAS, explore cohort overlaps, make overview plots of the data (upset plot)
Atlas Cohort Characterizations	Compare two or more cohorts e.g. according to conditions, drug usage, age, sex
LifeTrack	Visualize all health register data for a person in a single view

Tools for GWAS

Tool	Description
Custom GWAS tools	Tools to conduct user-defined custom GWAS
Pipelines	Pipeline is for large-scale unmodifiable, modifiable and user-defined analysis (pipelines) with parallelization and custom sized virtual machines
Cohort Operations	Custom GWAS tool pipeline can be launched also from Cohort Operations

Tools for genetic data browsing

Tool	Description
Genotype Browser	GenotypeBrowser is a graphical user interface to examine variant-level information within FinnGen Sandbox
PGS Browser	Browse and view polygenic scores for existing endpoints or a custom cohort
Exome query tool	A command line interface allowing users to query carriers of variants in FinnGen exome data

Other software and scripts

Tool	Description
Python packages	Python package installation instructions
R packages	R package installation instructions
Pre-installed Linux tools	Pre-installed basic (e.g. awk, grep) and FinnGen-specific Linux programs
Lmod linux tools	FinnGen-specific Linux programs loaded using Lmod
BigQuery	SQL queries
Superset	Explore FinnGen data stored in BiqQuery database
Jupyter	Interactive coding using python language and visualization of results in notebook style
PheWeb Users Input Validator tool	Validate the correct format of user-formatted input files to make custom GWAS summary stats viewable in a PheWeb-style
Sandbox internal API	Documentation for Sandbox internal API
Miscellaneous helper scripts/tools	Miscellaneous helper scripts and tools

See also a presentation of New FinGen tools and their application to example diseases from User's meeting 28th March 2023 recording (at 25min 23sec).