Export external site files to GenomeSpace

Certain GenomeSpace-enabled data portals, listed under Tools, allow direct export of their data to GenomeSpace to facilitate analysis of the data with other bioinformatic tools. These portals use a GenomeSpace lightweight data integration library (link for developers), which means you need to sign in to your separate account with the portal in order to access its data in any manner, including export.

Currently, data portals that offer direct export of their data to GenomeSpace include:

• The Cancer Cell Line Encyclopedia (CCLE) as detailed in the blogpost of September 30, 2013.
• The Multiple Myeloma Genomics Portal as detailed in the blogpost of September 24, 2013.
• Project Achilles
• InSilicoDB for certain datasets
• cBioPortal
• ArrayExpress

In general, a data portal will have a menu to browse data. For example, for the two first data portals above, access data from the menu bar Browse>Data. When data are listed at the file level, look for the small GenomeSpace icon next to each file name or at the bottom of the curation table. Clicking on the icon launches the GenomeSpace import dialog window.

• If prompted, login or register for GenomeSpace.
• Select the directory to save the file to and optionally rename the file.
• Click Submit.
• Analyze the data from GenomeSpace.

<< Extract file rows & columns | Up | Recipe demo datasets >>