Download TGCA expression data in the Galaxy Platform

Is this function implemented yet? Be glad to hear from your guys.

if you’re looking to get data from the Genomic Data Commons, there is a tool on, the GDCWebApp, which lets you import files into Galaxy. In the screenshot below, I typed GDC into the search bar to find it:

You can select TCGA datasets, narrow by disease (e.g., BRCA), and filter by a variety of parameters. It doesn’t seem to support protected data, which might be by design.

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Hi @Yugang_Fu

Update: We aren’t quite sure of the tool @sargentl shared will be successful or not. Tests are still running.

But the good news is that one of our PIs had alternative recommendations.

Here are a couple good links for downloading aggregated TCGA gene expression data. They all used different processing pipelines.

  1. Xena’s data hub
  1. Google Cloud

Hope that helps!

turns out the tools have not finished downloading the selected data overnight, so i would start with @jennaj’s suggestion