See Authentication for details. Once a user is logged in, controlled files that they have access to can be downloaded. To download files from the portal, users must agree to the GDC and individual project Data Use Agreements by selecting the agreement checkbox on the Access Alert message.
Any user can see a listing of all available data files, including controlled-access files. However, downloading of controlled-access files is restricted to authorized users and requires authentication.
After clicking Login, users authenticate themselves using their eRA Commons login and password. If authentication is successful, the eRA Commons username will be displayed in the upper right corner of the screen, in place of the "Login" button. The rest of this section describes controlled data access features of the GDC Data Portal available to authorized users. For more information about open and controlled-access data, and about obtaining access to controlled data, see Data Access Processes and Tools.
After logging into the GDC Portal, users can view which projects they have access to by clicking the User Profile section in the dropdown menu in the top corner of the screen. Once a file is finished downloading the extension will be removed. If an identical manifest is retried another attempt will be made to download files containing a. The user authentication token file needs to be specified using the -t or --token-file option.
The tool will first make a request to get the filename and project id from GDC API, and then upload the corresponding file from the current directory. Running the upload command again will resume the transfer of only those parts of the file that failed to upload in the previous attempt.
Previously uploaded data can be replaced with new data by deleting it first using the --delete switch:. This error message indicates that the user does not have dbGaP access to the project to which the file belongs. Instructions for requesting access from dbGaP can be found here. The graphic is updated as filters are applied for projects, programs, disease types, and data categories available in the project.
Note: Due to these filters, the number of cases displayed here will be less that the total number of cases per project. Hovering the cursor over each bar will display information about the number of cases affected by the disease type and clicking on each bar will launch the Gene Summary Page for the gene associated with the mutation.
Users can toggle the Y-Axis of this bar graph between a percentage or raw number of cases affected. A pie chart displays the relative number of cases for each project. Hovering the cursor over each portion of the graph will display the project with the number of associated cases. Filtering projects at the left panel will update the pie chart. The Table tab lists projects by Project ID and provides additional information about each project. If no facet filters have been applied, the table will display all available projects; otherwise it will display only those projects that match the selected criteria.
Columns with file and case counts include links to open the corresponding files or cases in Repository Page. Once all files of interest have been selected, click on the Cart button in the upper right-hand corner. This will bring up the cart page, which provides an overview of all currently selected files. This list of files can be downloaded as a manifest file by clicking on the green Download button and selecting Manifest from the drop down.
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