Desktop Applications in the Research Environment¶
The Research Environment has a number of applications on the desktop that will aid you in your analysis of the Genomics England dataset. These applications are accessible via desktop icons or through the Applications icon on the taskbar at the bottom of the screen.
Similarly, the Research Environment also has a number of whitelisted websites that will be accessible once inside the environment. You can request additional desktop applications or for websites to be whitelisted within the Research Environment by contacting the Genomics England Service Desk. Please be aware that we will not install desktop applications that are redundant with existing applications and we will not whitelist websites that may put the security of the Research Environment at risk.
For a list of command line software available, instructions on how to use the
module system, and requesting command line software, please see the High Performance Cluster (HPC) section of the documentation.
Below, you will see an up-to-date list of desktop applications within the Research Environment. Please find the respective subpages for specific applications.
List of AWS desktop applications¶
|LabKey||A software suite to access, integrate, and analyse the Genomics England clinical dataset.|
|Interactive Variant Analysis Tool (IVA)||A powerful variant catalog allowing for you to query genomic data using an intuitive web interface|
|Participant Explorer||The Genomics England Participant Explorer is a powerful tool that enables researchers to quickly and easily search for Main Programme participants by ID or by clinical concepts, and view their longitudinal health data.|
|Data Discovery Portal||The Data Discovery Portal allows you to browse and query the primary and clinical data available in the Research Environment using drop-down filters and interactive charts and graphs|
|PanelApp||A crowd sourcing tool to allow gene panels to shared, viewed and evaluated by the scientific community.|
|IGV Genome Browser||A high-performance visualisation tool for interactive exploration of large, integrated genomic datasets. Please note that the reference assemblies need to be manually loaded, as described here.|
|Home||Desktop file manager to navigate and access the files and folders that are available to you.|
|Firefox||Internet browser for whitelisted websites.|
|LibreOffice||A Microsoft Office-like suite of applications for data manipulation and presentation.|
|Terminal||The Linux command line interface.|
|R||A powerful and flexible programming language for statistical computing and graphics.|
|RStudio||An integrated development environment (IDE) for R.|
|PDF Viewer||Portable Document Format (PDF) viewer.|
|Rocket Chat||Rocket Chat is a chat facility that is available within the Research Environment to help you collaborate and communicate with other users.|
|File Transfer||An electronic form for you to request data transfer in and out of the Research Environment.|
|Research Environment Documentation||A link to the Research Environment documentation.|
You can request additional desktop applications within the RE by contacting the Genomics England Service Desk. Please be aware that we will not install desktop applications that are redundant with existing applications.