Package: UCSCXenaTools 1.6.1

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_1.6.1.tar.gz
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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:

XenaData - Xena Hub Information

On CRAN:

api-client bioinformatics ccle downloader icgc tcga toil treehouse ucsc ucsc-xena

9.16 score 109 stars 1 packages 244 scripts 1.5k downloads 4 mentions 28 exports 34 dependencies

Last updated 9 hours ago from:aae099fdb8 (on master). Checks:10 OK, 1 ERROR. Indexed: yes.

Target	Result	Total time
linux-devel-x86_64	OK	135
pkgdown docs	ERROR	145
source / vignettes	OK	177
linux-release-x86_64	OK	144
macos-release-arm64	OK	88
macos-oldrel-arm64	OK	85
windows-devel	OK	88
windows-release	OK	83
windows-oldrel	OK	83
wasm-release	OK	110
wasm-oldrel	OK	128

Exports:.XenaHub %>%availTCGA cohorts datasets downloadTCGA fetch fetch_dataset_identifiers fetch_dataset_samples fetch_dense_values fetch_sparse_values getTCGAdata has_probeMap hosts samples showTCGA to_snake xena_default_hosts XenaBrowse XenaDataUpdate XenaDownload XenaFilter XenaGenerate XenaHub XenaPrepare XenaQuery XenaQueryProbeMap XenaScan

Dependencies:askpass bit bit64 cli clipr cpp11 crayon curl digest dplyr generics glue hms httr jsonlite lifecycle magrittr mime openssl pillar pkgconfig prettyunits progress R6 readr rlang sys tibble tidyselect tzdb utf8 vctrs vroom withr

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 Aug 20 2025.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get or Check TCGA Available ProjectID, DataType and FileType	availTCGA
Get cohorts of XenaHub object	cohorts
Get datasets of XenaHub object	datasets
Easily Download TCGA Data by Several Options	downloadTCGA
Fetch Data from UCSC Xena Hosts	fetch fetch_dataset_identifiers fetch_dataset_samples fetch_dense_values fetch_sparse_values has_probeMap
Get TCGA Common Data Sets by Project ID and Property	getTCGAdata
Get hosts of XenaHub object	hosts
Get Samples of a XenaHub object according to 'by' and 'how' action arguments	samples
Show TCGA data structure by Project ID or ALL	showTCGA
Convert camel case to snake case	to_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 Hosts	xena_default_hosts
View Info of Dataset or Cohort at UCSC Xena Website Using Web browser	XenaBrowse
Xena Hub Information	XenaData
Get or Update Newest Data Information of UCSC Xena Data Hubs	XenaDataUpdate
Download Datasets from UCSC Xena Hubs	XenaDownload
Filter a XenaHub Object	XenaFilter
Generate and Subset a XenaHub Object from 'XenaData'	XenaGenerate
Generate a XenaHub Object	XenaHub
Class XenaHub	.XenaHub XenaHub-class
Prepare (Load) Downloaded Datasets to R	XenaPrepare
Query URL of Datasets before Downloading	XenaQuery
Query ProbeMap URL of Datasets	XenaQueryProbeMap
Scan all rows according to user input by a regular expression	XenaScan