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update xena data list
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ShixiangWang committed Oct 15, 2024
1 parent 12ccd29 commit 8462937
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: UCSCXenaTools
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Version: 1.5.0
Version: 1.6.0
Authors@R:
c(person(given = "Shixiang",
family = "Wang",
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5 changes: 5 additions & 0 deletions NEWS.md
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# UCSCXenaTools 1.6.0

- Single cell hub was found disabled.
- GDC hub was completely updated.

# UCSCXenaTools 1.5.0

- Bugs fixed.
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -77,7 +77,7 @@ Currently, **UCSCXenaTools** supports the following data hubs of UCSC Xena.
* UCSC Toil RNAseq Recompute Compendium Hub: <https://toil.xenahubs.net/>
* PCAWG Xena Hub: <https://pcawg.xenahubs.net/>
* ATAC-seq Hub: <https://atacseq.xenahubs.net/>
* Singel Cell Xena Hub: <https://singlecellnew.xenahubs.net/>
* Singel Cell Xena Hub: <https://singlecellnew.xenahubs.net/> (**Disabled by UCSCXena**)
* Kids First Xena Hub: <https://kidsfirst.xenahubs.net/>
* Treehouse Xena Hub: <https://xena.treehouse.gi.ucsc.edu:443/>

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5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -77,6 +77,7 @@ Xena.
- PCAWG Xena Hub: <https://pcawg.xenahubs.net/>
- ATAC-seq Hub: <https://atacseq.xenahubs.net/>
- Singel Cell Xena Hub: <https://singlecellnew.xenahubs.net/>
(**Disabled by UCSCXena**)
- Kids First Xena Hub: <https://kidsfirst.xenahubs.net/>
- Treehouse Xena Hub: <https://xena.treehouse.gi.ucsc.edu:443/>

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``` r
library(UCSCXenaTools)
#> =========================================================================================
#> UCSCXenaTools version 1.4.8
#> UCSCXenaTools version 1.5.0
#> Project URL: https://github.com/ropensci/UCSCXenaTools
#> Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
#>
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XenaQuery(df_todo) %>%
XenaDownload() -> xe_download
#> This will check url status, please be patient.
#> All downloaded files will under directory /var/folders/gm/lw6z28md2594gcnws_38_9f40000gn/T//RtmpfewSeZ.
#> All downloaded files will under directory /var/folders/37/gt0rbmqn61b513tbr8pyz_y40000gn/T//RtmpbXwIKj.
#> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
#> Creating directories for datasets...
#> Downloading TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
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