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 usegalaxy.org, 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.
- Xena’s data hub
- Google Cloud
- OSF | Google Cloud Pilot RNA-Sequencing for CCLE and TCGA
- from this paper: https://www.nature.com/articles/srep39259
Hope that helps!
turns out the tools have not finished downloading the selected data overnight, so i would start with @jennaj’s suggestion