├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── pr-commands.yaml ├── .gitignore ├── .lintr ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── Dockerfile ├── GEOquery.Rproj ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── GDS2MA.R ├── GEOquery-package.R ├── browseGEOAccession.R ├── classes.R ├── fileOpen.R ├── getGEO.R ├── getGEOSuppFiles.R ├── getGEOfile.R ├── getGSEDataTables.R ├── parseGEO.R ├── rnaseq.R ├── searchGEO.R └── zzz.R ├── README.md ├── _pkgdown.yml ├── inst ├── CITATION ├── extdata │ ├── GDS507.soft.gz │ ├── GPL97.annot.gz │ ├── GPLbroken.soft.gz │ ├── GSE781_family.soft.gz │ └── GSM11805.txt.gz └── scripts │ ├── buildGEODocsumJson.R │ └── geometa.R ├── man ├── GDS-class.Rd ├── GEOData-accessors.Rd ├── GEOData-class.Rd ├── GEODataTable-class.Rd ├── GPL-class.Rd ├── GSE-class.Rd ├── GSM-class.Rd ├── browseGEOAccession.Rd ├── browseWebsiteRNASeqSearch.Rd ├── coercion.Rd ├── extractFilenameFromDownloadURL.Rd ├── getDirListing.Rd ├── getGEO.Rd ├── getGEOSeriesFileListing.Rd ├── getGEOSuppFileURL.Rd ├── getGEOSuppFiles.Rd ├── getGEOfile.Rd ├── getGSEDataTables.Rd ├── getGSEDownloadPageURLs.Rd ├── getRNAQuantAnnotationURL.Rd ├── getRNAQuantRawCountsURL.Rd ├── getRNASeqData.Rd ├── getRNASeqQuantGenomeInfo.Rd ├── getRNASeqQuantResults.Rd ├── hasRNASeqQuantifications.Rd ├── parseGEO.Rd ├── parseGSEMatrix.Rd ├── readRNAQuantAnnotation.Rd ├── readRNAQuantRawCounts.Rd ├── searchFieldsGEO.Rd ├── searchGEO.Rd ├── urlExtractRNASeqQuantGenomeInfo.Rd └── urlForAccession.Rd ├── tests ├── testthat.R └── testthat │ ├── test_GDS.R │ ├── test_GEO_conversions.R │ ├── test_GPL.R │ ├── test_GSE.R │ ├── test_GSM.R │ ├── test_fetch_GPL_false.R │ ├── test_geo_browse.R │ ├── test_geo_rnaseq.R │ ├── test_search.R │ └── test_supp_files.R └── vignettes ├── .gitignore ├── GEOquery.qmd └── single-cell.qmd /.Rbuildignore: 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