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ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
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Error downloading CCLE datasets from publicHub #25

Closed vuzun closed 4 years ago

vuzun commented 4 years ago

Hi,

I'm trying to download CCLE files, but I get the file missing message:

cannot open URL 'https://ucscpublic.xenahubs.net/download/ccle/CCLE_copynumber_2013-12-03.seg.txt': HTTP status was '404 Not Found'

The code I use:

mysets <- XenaGenerate(subset = XenaHostNames=="publicHub") %>%
    XenaFilter(filterCohorts = "CCLE")
XenaQuery(mysets) %>%
    XenaDownload() -> ccle_download

If I try the same with MAGIC datasets, it works fine.

github-actions[bot] commented 4 years ago

Thanks for reporting, Shixiang will reply as soon as possible:)

ShixiangWang commented 4 years ago

@vuzun Thanks for reporting, there are some problems for querying the data. I need to contact with the UCSC Xena team.

I will let you know if it is fixed.

ShixiangWang commented 4 years ago

@vuzun Sorry for the late reply, I forgot the response from Xena team. I am sorry to tell you that the CCLE cohort can not be downloaded by UCSCXenaTools due to the permission.

The response is:

Hi Shixiang,

So great to hear from you! Unfortunately we are not authorized to provide downloads of the CCLE data. CCLE wants users of the data to go through them instead.

Let me know if there's anything else I can help with!

Best, Mary

I recommend you downloaded raw datasets from https://data.broadinstitute.org/ccle/ or https://portals.broadinstitute.org/ccle/data (need login)