The tranSMART application reflects the efforts of various informatics groups to integrate data from internal and external data sources within a single data warehouse. It provides scientific end users the tools to search for, view and analyze the data in the warehouse.
The core, internal data is a historical base of biomarker data from gene expression, RBM and SNP experiments involving GWAS, Metabolic GWAS and eQTL data types and including both raw and analyzed data.
The tranSMART application includes a search tool that lets researchers query this vast ocean of disparate data for studies of interest and related resources.
Another major tranSMART feature, called Analyze, allows authorized users to create and study cohorts of patients that have been involved in completed clinical research efforts. Analyze includes an Across Trials feature that allows users to define cohorts made up of patients from multiple studies.
There may be some minor differences between the UI objects illustrated in this guide and the ones you see on your screen.
The tranSMART menu bar contains the following tools:
- Browse — Search across studies and analyses for research data related to filters that you specify.
- Analyze — View study data for subjects that you select, based on criteria that you specify. Also, compare data generated for subjects in two different cohorts, based on criteria and points of comparison that you specify.
- Sample Explorer — Search for datasets of tested tissue and blood samples, within categories such as tissue type, pathology and test type (e.g. gene expression or SNP).
- Gene Signature/Lists — View definitions of existing gene signatures and add new gene signature definitions.
- GWAS — View genetic variants in individuals to find those that may be associated with a trait of interest, such as a major disease.
- Upload Data — Upload analysis data for a study.
- Admin — (If applicable) Perform administrative tasks such as creating tranSMART user accounts.
- Utilities — Contains Help, contact link, information about tranSMART, change password and logout functionality.
To log into tranSMART:
- Type the address of the tranSMART software into your browser’s URL field. The login screen appears:
- Type your tranSMART login credentials and click Login.
- Original text https://github.com/tranSMART-Foundation/transmartApp-doc/blob/master/source/getting_started.rst
- Hyve manual website http://transmart-app.readthedocs.io/en/latest/
- i2b2 tranSMART Foundation website https://transmartfoundation.org/