Tools Library

The Our Future Health Trusted Research Environment provides a full-featured toolkit for preparing and analyzing a wide range of datatypes..

About the Tools Library

The Tools Library under the Tools tab of the platform shows a complete list of apps and workflows available to you. Use filters to quickly find items by name, category, etc.

Using Tools in Restricted Projects

When working in any project that contains OFH study data, there are restrictions on data usage, downloads, uploads, and file previews. These restrictions apply also to all tools accessible via the TRE, such as the Cohort Browser, JupyterLab, and other tools available via the Tools Library.

See the Creating a Project page for more detail on these restrictions.

Learning about Individual Apps

Clicking on the name of an app will open up a separate information page which contains details about the app's inputs, outputs, and other documentation details. For apps encapsulating existing bioinformatics tools this page also contains licensing information, links to the website for that software, and citations to any related publications. This page also shows the version history for the app and developer documentation which describes the inner workings of the app in detail.

Genomics Apps

  • Swiss Army Knife, which provides access to the following tools:

    • BCFtools

    • BEDtools

    • BOLT-LMM

    • VCFtools

    • vcflib

    • PLINK

    • PLINK2

    • Sambamba

    • SAMtools

    • Picard

    • Plato

    • Tabix

    • Seqtk

    • bgzip

    • Regenie


Translational Analysis Apps

Statistical Analysis

Image Processing

  • JupyterLab app with the IMAGE_PROCESSING feature provides access to:

    • nipype

    • FreeSurfer

    • FSL

Machine Learning (ML)

Utility Apps

Dataset Management Apps

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