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
PLINK GWAS
Translational Analysis Apps
JupyterLab with R and JupyterLab with Spark Cluster provide access to the following R packages:
BiocManager
MendelianRandomization
coloc
HyPrColoc
epiR
prevalence
incidence
outbreaks
JupyterLab with Spark Cluster provides access to:
Hail
VEP
Glow
koalas
pyarrow
Bokeh
sparklyr
Statistical Analysis
JupyterLab app with PYTHON_R and JupyterLab with Spark Cluster app provide access to:
NumPy
SciPy
Matplotlib
Seaborn
Pandas
JupyterLab with Stata provides access to:
Stata (license to be provided by the user)
Image Processing
JupyterLab app with the IMAGE_PROCESSING feature provides access to:
nipype
FreeSurfer
FSL
Machine Learning (ML)
JupyterLab app with ML provides access to:
tensorflow
torch
cntk
keras
scikit-learn
JupyterLab with Spark Cluster provides access to the following tools:
MLlib
Utility Apps
AWS S3 Importer transfers files from S3 bucket to the platform.
AWS S3 Exporter uploads files into an external S3 bucket.
Cloud Workstation provides an SSH-accessible workstation.
URL Fetcher fetches and uploads a file from a remote URL to the platform.
Dataset Management Apps
Rebase Cohorts And Dashboards rebases cohorts and or dashboards onto the provided target dataset.
Table Exporter exports a Spark SQL database table to a CSV file.
Dataset Extender ingest a data file and create a new superset Dataset
Spark SQL Runner runs generic Spark SQL commands.
Data Model Loader use a custom data model to guide CSV file ingestion.
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