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:
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 site:https://docs.ropensci.org
- XenaData - Xena Hub Information
api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
Last updated from:a3f2b8ce63 (on master). Checks:9 OK, 1 ERROR. Indexed: yes.
| Target | Result | Total time | Artifact |
|---|---|---|---|
| linux-devel-x86_64 | OK | 137 | |
| pkgdown docs | ERROR | 146 | |
| source / vignettes | OK | 189 | |
| linux-release-x86_64 | OK | 136 | |
| macos-release-arm64 | OK | 99 | |
| macos-oldrel-arm64 | OK | 125 | |
| windows-devel | OK | 99 | |
| windows-release | OK | 107 | |
| windows-oldrel | OK | 84 | |
| wasm-release | OK | 114 |
Exports:.XenaHub%>%availTCGAcohortsdatasetsdownloadTCGAfetchfetch_dataset_identifiersfetch_dataset_samplesfetch_dense_valuesfetch_sparse_valuesgetTCGAdatahas_probeMaphostssamplesshowTCGAto_snakexena_default_hostsXenaBrowseXenaDataUpdateXenaDownloadXenaFilterXenaGenerateXenaHubXenaPrepareXenaQueryXenaQueryProbeMapXenaScan
Dependencies:askpassbitbit64clicliprcpp11crayoncurldigestdplyrgenericsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogressR6readrrlangsystibbletidyselecttzdbutf8vctrsvroomwithr
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 |
