Package: GEOquery 2.81.21
GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)
The NCBI Gene Expression Omnibus (GEO) is a public repository of high-throughput functional genomics data, including microarray, RNA-seq, and single-cell experiments. GEOquery is the bridge between GEO and Bioconductor: it downloads and parses GEO Series (GSE), Sample (GSM), Platform (GPL), and DataSet (GDS) records. By default it parses GEO Series Matrix files into Bioconductor 'ExpressionSet' objects; it can also parse the full SOFT format into GEOquery's own S4 classes, retrieve NCBI-computed RNA-seq quantifications, download supplementary files, and search GEO.
Authors:
GEOquery_2.81.21.tar.gz
GEOquery_2.81.21.zip(r-4.7)GEOquery_2.81.21.zip(r-4.6)GEOquery_2.81.21.zip(r-4.5)
GEOquery_2.81.21.tgz(r-4.6-any)GEOquery_2.81.0.tgz(r-4.5-any)
GEOquery_2.81.21.tar.gz(r-4.7-any)GEOquery_2.81.21.tar.gz(r-4.6-any)
GEOquery_2.81.21.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GEOquery/json (API)
| # Install 'GEOquery' in R: |
| install.packages('GEOquery', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/seandavi/geoquery/issues
Pkgdown/docs site:https://seandavi.github.io
On BioConductor:GEOquery-2.81.0(bioc 3.24)GEOquery-2.80.0(bioc 3.23)
geneexpressiontranscriptomicsmicroarrayrnaseqsequencingsinglecelldataimportthirdpartyclientonechanneltwochannelsagebioconductorbioinformaticsdata-sciencegenomicsncbi-geou24ca289073quarto
Last updated from:0d487a73b3. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 189 | ||
| linux-devel-x86_64 | NOTE | 335 | ||
| source / vignettes | OK | 283 | ||
| linux-release-x86_64 | NOTE | 334 | ||
| macos-release-arm64 | NOTE | 209 | ||
| macos-oldrel-arm64 | NOTE | 184 | ||
| windows-devel | NOTE | 268 | ||
| windows-release | NOTE | 264 | ||
| windows-oldrel | NOTE | 294 | ||
| wasm-release | OK | 158 |
Exports:Accessionas_SummarizedExperimentbrowseGEOAccessionbrowseWebsiteRNASeqSearchclearGEOCacheColumnsdataTableGDS2eSetGDS2MAgeoCachegeoSingleCellManifestgeoSingleCellUnitsgetGEOgetGEOfilegetGEOSeriesFileListinggetGEOSingleCellgetGEOSuppFilesgetGEOSuppFileURLgetGSEDataTablesgetRNASeqDatagetRNASeqQuantGenomeInfoGPLGPLListGSMListhasRNASeqQuantificationsMetaparseGEOreadGEOSingleCellsearchFieldsGEOsearchGEOshowTableurlForAccession
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicliprcpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrfastmapfilelockgenericsGenomicRangesgluehmshttrhttr2IRangesjsonlitelatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsreadrrentrezrlangRSQLitervestS4ArraysS4VectorsselectrSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrXMLxml2XVector
