Package: GEOquery 2.75.0
Sean Davis
GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)
The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.
Authors:
GEOquery_2.75.0.tar.gz
GEOquery_2.75.0.zip(r-4.5)GEOquery_2.75.0.zip(r-4.4)GEOquery_2.75.0.zip(r-4.3)
GEOquery_2.75.0.tgz(r-4.4-any)GEOquery_2.75.0.tgz(r-4.3-any)
GEOquery_2.75.0.tar.gz(r-4.5-noble)GEOquery_2.75.0.tar.gz(r-4.4-noble)
GEOquery_2.75.0.tgz(r-4.4-emscripten)GEOquery_2.75.0.tgz(r-4.3-emscripten)
GEOquery.pdf |GEOquery.html✨
GEOquery/json (API)
NEWS
| # 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 site:https://seandavi.github.io
On BioConductor:GEOquery-2.75.0(bioc 3.21)GEOquery-2.74.0(bioc 3.20)
microarraydataimportonechanneltwochannelsagebioconductorbioinformaticsdata-sciencegenomicsncbi-geo
Last updated 3 months agofrom:2a416df48b. Checks:1 OK, 5 NOTE, 1 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Dec 29 2024 |
| R-4.5-win | ERROR | Dec 31 2024 |
| R-4.5-linux | NOTE | Dec 29 2024 |
| R-4.4-win | NOTE | Dec 31 2024 |
| R-4.4-mac | NOTE | Dec 29 2024 |
| R-4.3-win | NOTE | Dec 31 2024 |
| R-4.3-mac | NOTE | Dec 29 2024 |
Exports:AccessionbrowseGEOAccessionbrowseWebsiteRNASeqSearchColumnsdataTableGDS2eSetGDS2MAgetGEOgetGEOfilegetGEOSuppFilesgetGSEDataTablesgetRNASeqDatagetRNASeqQuantGenomeInfoGPLGPLListGSMListhasRNASeqQuantificationsMetaparseGEOsearchFieldsGEOsearchGEOshowTableurlForAccession
Dependencies:abindaskpassBiobaseBiocGenericsbitbit64clicliprcpp11crayoncurldata.tableDelayedArraydplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehmshttrhttr2IRangesjsonlitelatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsreadrrentrezrlangrvestS4ArraysS4VectorsselectrSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2XVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Open the GEO page for a given accession | browseGEOAccession |
| Browse GEO search website for RNA-seq datasets | browseWebsiteRNASeqSearch |
| Convert a GDS data structure to a BioConductor data structure | coercion GDS2eSet GDS2MA |
| Class 'GDS' | GDS-class |
| Generic functions for GEOquery | Accession Columns dataTable GEOData-accessors GPLList GSMList Meta Table |
| Class 'GEOData' | Accession,GEOData-method Columns,GEOData-method dataTable,GEOData-method GEOData-class Meta,GEOData-method show,GEOData-method Table,GEOData-method |
| Class 'GEODataTable' | Accession,GEODataTable-method Columns,GEODataTable-method dataTable,GEODataTable-method GEODataTable-class Meta,GEODataTable-method show,GEODataTable-method Table,GEODataTable-method |
| get a directory listing from NCBI GEO | getDirListing |
| Get a GEO object from NCBI or file | getGEO |
| Download a file from GEO soft file to the local machine | getGEOfile |
| Get Supplemental Files from GEO | getGEOSuppFiles |
| Get GSE data tables from GEO into R data structures. | getGSEDataTables |
| Get GEO RNA-seq quantifications as a SummarizedExperiment object | getRNASeqData |
| Extract genome build and species for GEO RNA-seq quantification | getRNASeqQuantGenomeInfo |
| Class 'GPL' | GPL GPL,GDS-method GPL-class |
| Class 'GSE' | GPLList,GSE-method GSE-class GSMList,GSE-method Meta,GSE-method |
| Class 'GSM' | GSM-class |
| Does a GEO accession have RNA-seq quantifications? | hasRNASeqQuantifications |
| Parse GEO text | parseGDS parseGEO parseGPL parseGSE parseGSM |
| Provide a list of possible search fields for GEO search | searchFieldsGEO |
| Search GEO database | searchGEO |
| The URL for a GEO accession | urlForAccession |
