Get all the samples and probes of a dataset

[Genaro Camele]

Hello,

First of all, thanks for this platform.

I'm writing to ask if it is possible through the Python API to access all the complete information (for example, all the samples with all the genes) of a particular dataset. Because so far the functions we found only allow us to get the expressions from a list of samples and molecules.
For example, currently we can do dataset_probe_values(dataset, samples, probes)
But I would like to be able to do dataset_probe_values(dataset) and get all the samples and probes available in it. Is it currently possible?

Thank you very much in advance

[Mary Goldman]

Hello,

It sounds like you are trying to download a whole dataset. We provide bulk downloads from our dataset pages here: https://xenabrowser.net/datapages/ If you click down to a dataset there will be a URL to the bulk download. 

Please let me know if this does not resolve your issue.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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[Genaro Camele]

Hi Mary,

First of all, thanks for your quick response. 

Secondly, we have already seen that we can download the files from the web, but we would like to do it programmatically through Python. Do you think it is possible?

Regards

[Mary Goldman]

Hello,

Sorry, our API is designed to give users slices of the data, not the whole dataset. That said, you could instead download the file using a Python library such as the Requests library.

Best,

To view this discussion on the web visit https://groups.google.com/d/msgid/ucsc-cancer-genomics-browser/46b257c9-f099-4cba-8d82-6a63c82cb8c6n%40googlegroups.com.