Which tools are available?
Last updated
Last updated
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 finngen-servicedesk@helsinki.fi.
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.
Many tools installed in the Sandbox are available in the Applications menu (see the screenshot below):
Create user-defined cohorts and inspect them visually and through characterizations, export cohorts
Operate cohorts made with other tools (e.g. Atlas, Genotype Browser, R), export cohorts, visualization
Create cohorts based on genotype content
Visualize large numbers of longitudinal cases with glyphs of user-defined conditions: Timeline viewer, Overview plots of the data, Upset plot, export cohorts & glyphs
Explore code and endpoint enrichments using CodeWAS and TimeCodeWAS, explore cohort overlaps, make overview plots of the data (upset plot)
Compare two or more cohorts e.g. according to conditions, drug usage, age, sex
Visualize all health register data for a person in a single view
Tools to conduct user-defined custom GWAS
Pipeline is for large-scale unmodifiable, modifiable and user-defined analysis (pipelines) with parallelization and custom sized virtual machines
Custom GWAS tool pipeline can be launched also from Cohort Operations
GenotypeBrowser is a graphical user interface to examine variant-level information within FinnGen Sandbox
Browse and view polygenic scores for existing endpoints or a custom cohort
A command line interface allowing users to query carriers of variants in FinnGen exome data
Python package installation instructions
R package installation instructions
Pre-installed basic (e.g. awk, grep) and FinnGen-specific Linux programs
FinnGen-specific Linux programs loaded using Lmod
SQL queries
Explore FinnGen data stored in BiqQuery database
Interactive coding using python language and visualization of results in notebook style
Validate the correct format of user-formatted input files to make custom GWAS summary stats viewable in a PheWeb-style
Documentation for Sandbox internal API
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).
