Package: UCSCXenaTools 1.6.2

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_1.6.2.tar.gz
UCSCXenaTools_1.6.2.zip(r-4.6)UCSCXenaTools_1.6.2.zip(r-4.5)UCSCXenaTools_1.6.2.zip(r-4.4)
UCSCXenaTools_1.6.2.tgz(r-4.5-any)UCSCXenaTools_1.6.2.tgz(r-4.4-any)
UCSCXenaTools_1.6.2.tar.gz(r-4.6-any)UCSCXenaTools_1.6.2.tar.gz(r-4.5-any)
UCSCXenaTools_1.6.2.tgz(r-4.5-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/docs site:https://docs.ropensci.org

Datasets:

On CRAN:

Conda:

api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena

9.41 score 109 stars 1 packages 249 scripts 2.3k downloads 4 mentions 28 exports 34 dependencies

Last updated from:830b0bf63c (on master). Checks:10 OK. Indexed: yes.

TargetResultTotal timeArtifact
linux-devel-x86_64OK148
pkgdown docsOK164
source / vignettesOK342
linux-release-x86_64OK135
macos-release-arm64OK112
macos-oldrel-arm64OK128
windows-develOK93
windows-releaseOK96
windows-oldrelOK98
wasm-releaseOK122

Exports:.XenaHub%>%availTCGAcohortsdatasetsdownloadTCGAfetchfetch_dataset_identifiersfetch_dataset_samplesfetch_dense_valuesfetch_sparse_valuesgetTCGAdatahas_probeMaphostssamplesshowTCGAto_snakexena_default_hostsXenaBrowseXenaDataUpdateXenaDownloadXenaFilterXenaGenerateXenaHubXenaPrepareXenaQueryXenaQueryProbeMapXenaScan

Dependencies:askpassbitbit64clicliprcpp11crayoncurldigestdplyrgenericsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogressR6readrrlangsystibbletidyselecttzdbutf8vctrsvroomwithr

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 Oct 07 2025.

Last update: 2025-08-19
Started: 2018-08-19

Readme and manuals

Help Manual

Help pageTopics
Get or Check TCGA Available ProjectID, DataType and FileTypeavailTCGA
Get cohorts of XenaHub objectcohorts
Get datasets of XenaHub objectdatasets
Easily Download TCGA Data by Several OptionsdownloadTCGA
Fetch Data from UCSC Xena Hostsfetch fetch_dataset_identifiers fetch_dataset_samples fetch_dense_values fetch_sparse_values has_probeMap
Get TCGA Common Data Sets by Project ID and PropertygetTCGAdata
Get hosts of XenaHub objecthosts
Get Samples of a XenaHub object according to 'by' and 'how' action argumentssamples
Show TCGA data structure by Project ID or ALLshowTCGA
Convert camel case to snake caseto_snake
UCSC Xena Dynamic Objects.p_all_cohorts .p_all_datasets .p_all_datasets_n .p_all_field_metadata .p_cohort_samples .p_cohort_summary .p_datasets_null_rows .p_dataset_fetch .p_dataset_field .p_dataset_field_examples .p_dataset_field_n .p_dataset_gene_probes_values .p_dataset_gene_probe_avg .p_dataset_list .p_dataset_metadata .p_dataset_probe_signature .p_dataset_probe_values .p_dataset_samples .p_dataset_samples_ndense_matrix .p_dataset_sources .p_dataset_status .p_feature_list .p_field_codes .p_field_metadata .p_gene_transcripts .p_match_fields .p_probemap_list .p_probe_count .p_ref_gene_exons .p_ref_gene_position .p_ref_gene_range .p_segmented_data_range .p_segment_data_examples .p_sparse_data .p_sparse_data_examples .p_sparse_data_match_field .p_sparse_data_match_field_slow .p_sparse_data_match_partial_field .p_sparse_data_range .p_transcript_expression .xq_all_cohorts .xq_all_datasets .xq_all_datasets_n .xq_all_field_metadata .xq_cohort_samples .xq_cohort_summary .xq_datasets_null_rows .xq_dataset_fetch .xq_dataset_field .xq_dataset_field_examples .xq_dataset_field_n .xq_dataset_gene_probes_values .xq_dataset_gene_probe_avg .xq_dataset_list .xq_dataset_metadata .xq_dataset_probe_signature .xq_dataset_probe_values .xq_dataset_samples .xq_dataset_samples_ndense_matrix .xq_dataset_sources .xq_dataset_status .xq_feature_list .xq_field_codes .xq_field_metadata .xq_gene_transcripts .xq_match_fields .xq_probemap_list .xq_probe_count .xq_ref_gene_exons .xq_ref_gene_position .xq_ref_gene_range .xq_segmented_data_range .xq_segment_data_examples .xq_sparse_data .xq_sparse_data_examples .xq_sparse_data_match_field .xq_sparse_data_match_field_slow .xq_sparse_data_match_partial_field .xq_sparse_data_range .xq_transcript_expression UCSCXenaTools-dynamic
UCSC Xena Default Hostsxena_default_hosts
View Info of Dataset or Cohort at UCSC Xena Website Using Web browserXenaBrowse
Xena Hub InformationXenaData
Get or Update Newest Data Information of UCSC Xena Data HubsXenaDataUpdate
Download Datasets from UCSC Xena HubsXenaDownload
Filter a XenaHub ObjectXenaFilter
Generate and Subset a XenaHub Object from 'XenaData'XenaGenerate
Generate a XenaHub ObjectXenaHub
Class XenaHub.XenaHub XenaHub-class
Prepare (Load) Downloaded Datasets to RXenaPrepare
Query URL of Datasets before DownloadingXenaQuery
Query ProbeMap URL of DatasetsXenaQueryProbeMap
Scan all rows according to user input by a regular expressionXenaScan