Package: UCSCXenaTools 1.6.0

Shixiang Wang

UCSCXenaTools: Download and Explore Datasets from UCSC Xena Data Hubs

Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.

Authors:Shixiang Wang [aut, cre], Xue-Song Liu [aut], Martin Morgan [ctb], Christine Stawitz [rev], Carl Ganz [rev]

UCSCXenaTools_1.6.0.tar.gz
UCSCXenaTools_1.6.0.zip(r-4.6)UCSCXenaTools_1.6.0.zip(r-4.5)UCSCXenaTools_1.6.0.zip(r-4.4)
UCSCXenaTools_1.6.0.tgz(r-4.5-any)UCSCXenaTools_1.6.0.tgz(r-4.4-any)
UCSCXenaTools_1.6.0.tar.gz(r-4.6-any)UCSCXenaTools_1.6.0.tar.gz(r-4.5-any)
UCSCXenaTools_1.6.0.tgz(r-4.4-emscripten)
UCSCXenaTools.pdf |UCSCXenaTools.html✨
UCSCXenaTools/json (API)
NEWS

# Install 'UCSCXenaTools' in R:
install.packages('UCSCXenaTools', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #315

Bug tracker:https://github.com/ropensci/ucscxenatools/issues

Pkgdown site:https://docs.ropensci.org

Datasets:

On CRAN:

Conda:

api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena

8.66 score 108 stars 1 packages 237 scripts 722 downloads 4 mentions 28 exports 35 dependencies

Last updated 7 months agofrom:aa33f6f951 (on master). Checks:10 OK. Indexed: yes.

TargetResultTotal time
source / vignettesOK263
pkgdown docsOK455
linux-devel-x86_64OK251
linux-release-x86_64OK395
macos-release-arm64OK75
macos-oldrel-arm64OK81
windows-develOK86
windows-releaseOK73
windows-oldrelOK78
wasm-releaseOK186

Exports:.XenaHub%>%availTCGAcohortsdatasetsdownloadTCGAfetchfetch_dataset_identifiersfetch_dataset_samplesfetch_dense_valuesfetch_sparse_valuesgetTCGAdatahas_probeMaphostssamplesshowTCGAto_snakexena_default_hostsXenaBrowseXenaDataUpdateXenaDownloadXenaFilterXenaGenerateXenaHubXenaPrepareXenaQueryXenaQueryProbeMapXenaScan

Dependencies:askpassbitbit64clicliprcpp11crayoncurldigestdplyrfansigenericsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogressR6readrrlangsystibbletidyselecttzdbutf8vctrsvroomwithr

UCSCXenaTools: an R package for Accessing Genomics Data from UCSC Xena platform, from Cancer Multi-omics to Single-cell RNA-seq

Shixiang Wang ShanghaiTech University

Rendered fromUSCSXenaTools.Rmdusingknitr::rmarkdownon May 29 2025.

Last update: 2024-01-13
Started: 2018-08-19