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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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XenaQuery throws error #37

Closed Amhaslam closed 2 years ago

Amhaslam commented 2 years ago

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github-actions[bot] commented 2 years ago

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

ShixiangWang commented 2 years ago

@Amhaslam This is typically caused by bad internet. You can retry it after a while. Also could you show all your query code, so I can try reproducing this?

Amhaslam commented 2 years ago

thank you for your immediate response, image

ShixiangWang commented 2 years ago

@Amhaslam Hi, this works for me. So you need to check your internet of R to the UCSC data hubs. Or download it with web browser from https://xenabrowser.net/datapages/?cohort=TCGA%20TARGET%20GTEx&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

library(UCSCXenaTools)
data("XenaData")
GEC_toil = XenaGenerate(subset = XenaHostNames == "toilHub") |> 
    XenaFilter(filterDatasets = "TcgaTargetGtex_gene_expected_count")

GEC_toil %>%
    XenaQuery() %>%
    XenaDownload(destdir = "~/../Downloads/")

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