├── .Rbuildignore ├── .github └── workflows │ ├── greetings.yml │ └── main.yml ├── .gitignore ├── CRAN-RELEASE ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── XenaBrowse.R ├── XenaDownload.R ├── XenaFilter.R ├── XenaGenerate.R ├── XenaHub-class.R ├── XenaPrepare.R ├── XenaQuery.R ├── XenaQueryProbeMap.R ├── XenaScan.R ├── api_higher.R ├── api_inner.R ├── api_xq.R ├── data.R ├── dynamics.R ├── fetch.R ├── simplify.R ├── utils-pipe.R ├── utils.R └── zzz.R ├── README.Rmd ├── README.md ├── UCSCXenaTools.Rproj ├── _pkgdown.yml ├── data-raw └── mirror.R ├── data └── XenaData.rda ├── inst ├── CITATION ├── api.RData ├── dataset_metadata.RData ├── develop.R ├── queries │ ├── allCohorts.xq │ ├── allDatasets.xq │ ├── allDatasetsN.xq │ ├── allFieldMetadata.xq │ ├── cohortSamples.xq │ ├── cohortSummary.xq │ ├── datasetFetch.xq │ ├── datasetField.xq │ ├── datasetFieldExamples.xq │ ├── datasetFieldN.xq │ ├── datasetGeneProbeAvg.xq │ ├── datasetGeneProbesValues.xq │ ├── datasetList.xq │ ├── datasetMetadata.xq │ ├── datasetProbeSignature.xq │ ├── datasetProbeValues.xq │ ├── datasetSamples.xq │ ├── datasetSamplesNDenseMatrix.xq │ ├── datasetSources.xq │ ├── datasetStatus.xq │ ├── datasetsNullRows.xq │ ├── featureList.xq │ ├── fieldCodes.xq │ ├── fieldMetadata.xq │ ├── geneTranscripts.xq │ ├── matchFields.xq │ ├── probeCount.xq │ ├── probemapList.xq │ ├── refGeneExons.xq │ ├── refGenePosition.xq │ ├── refGeneRange.xq │ ├── segmentDataExamples.xq │ ├── segmentedDataRange.xq │ ├── sparseData.xq │ ├── sparseDataExamples.xq │ ├── sparseDataMatchField.xq │ ├── sparseDataMatchFieldSlow.xq │ ├── sparseDataMatchPartialField.xq │ ├── sparseDataRange.xq │ └── transcriptExpression.xq └── test_api.R ├── man ├── UCSCXenaTools-dynamic.Rd ├── XenaBrowse.Rd ├── XenaData.Rd ├── XenaDataUpdate.Rd ├── XenaDownload.Rd ├── XenaFilter.Rd ├── XenaGenerate.Rd ├── XenaHub-class.Rd ├── XenaHub.Rd ├── XenaPrepare.Rd ├── XenaQuery.Rd ├── XenaQueryProbeMap.Rd ├── XenaScan.Rd ├── availTCGA.Rd ├── cohorts.Rd ├── datasets.Rd ├── downloadTCGA.Rd ├── fetch.Rd ├── figures │ └── logo.png ├── getTCGAdata.Rd ├── hosts.Rd ├── pipe.Rd ├── samples.Rd ├── showTCGA.Rd ├── to_snake.Rd └── xena_default_hosts.Rd ├── paper ├── overview.png ├── paper.Rmd ├── paper.bib └── paper.md ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── testthat.R └── testthat │ ├── test-basic-workflow.R │ └── test-full-tests.R └── vignettes ├── .gitignore └── USCSXenaTools.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ropensci/UCSCXenaTools/HEAD/.Rbuildignore 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