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-4.5)UCSCXenaTools_1.6.0.zip(r-4.4)UCSCXenaTools_1.6.0.zip(r-4.3)
UCSCXenaTools_1.6.0.tgz(r-4.5-any)UCSCXenaTools_1.6.0.tgz(r-4.4-any)UCSCXenaTools_1.6.0.tgz(r-4.3-any)
UCSCXenaTools_1.6.0.tar.gz(r-4.5-noble)UCSCXenaTools_1.6.0.tar.gz(r-4.4-noble)
UCSCXenaTools_1.6.0.tgz(r-4.4-emscripten)UCSCXenaTools_1.6.0.tgz(r-4.3-emscripten)
UCSCXenaTools.pdf |UCSCXenaTools.html✨
UCSCXenaTools/json (API)
NEWS

# Install 'UCSCXenaTools' in R:
install.packages('UCSCXenaTools', repos = c('https://ropensci.r-universe.dev', '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

8.50 score 107 stars 1 packages 163 scripts 797 downloads 4 mentions 28 exports 35 dependencies

Last updated 4 months agofrom:aa33f6f951 (on master). Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 12 2025
R-4.5-winOKFeb 19 2025
R-4.5-macOKFeb 12 2025
R-4.5-linuxOKFeb 12 2025
R-4.4-winOKFeb 12 2025
R-4.4-macOKFeb 12 2025
R-4.3-winOKFeb 12 2025
R-4.3-macOKFeb 12 2025

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 Feb 12 2025.

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