Installation | A quick example | Backends | Search | Find the values a filter accepts | Get detailed metadata for a project | Enriched (ontology-annotated) metadata | Sample cohorts across every project | Filtering on what the reads contain | Publications | BibTeX export | Growth of scRNA-seq and snRNA-seq datasets | Finding PBMC scRNA-seq datasets with BAM files | Cumulative project deposits across databases | Using SQL and dplyr directly | Cache tables locally | Close connection
Package: seqout 0.1.0
Saket Choudhary
seqout: Client for Querying the 'SeqOut' Genomics Metadata Database
Search and download genomics study metadata from 'SeqOut' <https://seqout.org>, which indexes NCBI GEO, NCBI SRA, EBI ENA, DDBJ (DRA and GEA), ArrayExpress and GSA.
Authors:
seqout_0.1.0.tar.gz
seqout_0.1.0.zip(r-4.7-any)seqout_0.1.0.zip(r-4.6-any)seqout_0.1.0.zip(r-4.5-any)
seqout_0.1.0.tgz(r-4.6-any)seqout_0.1.0.tgz(r-4.5-any)
seqout_0.1.0.tar.gz(r-4.7-any)seqout_0.1.0.tar.gz(r-4.6-any)
seqout_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
seqout/json (API)
| # Install 'seqout' in R: |
| install.packages('seqout', repos = c('https://saketlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/saketlab/seqout/issues
Pkgdown/docs site:https://seqout.org
Last updated from:cbb03c212c (on master). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 267 | ||
| source / vignettes | OK | 1668 | ||
| linux-release | OK | 233 | ||
| macos-release | OK | 109 | ||
| macos-oldrel | OK | 109 | ||
| windows-devel | OK | 135 | ||
| windows-release | OK | 132 | ||
| windows-oldrel | OK | 132 | ||
| wasm-release | OK | 181 |
Exports:accession_kindAccessionKindassay_projectsAssayProjectsauthorAuthorbind_countsBindCountsbulk_metadatabulk_project_metadatabulk_searchBulkMetadataBulkProjectMetadataBulkSearchcache_tableCacheTablecellxgene_countscheck_sra_bamCheckSraBamclassifyClassifyclear_cacheClearCachecommon_nameCommonNamecounts_matrixCountsMatrixdatasetDatasetdownload_filesdownload_runsdownload_scriptdownload_supplementaryDownloadFilesDownloadRunsDownloadScriptDownloadSupplementaryexperiment_runsExperimentRunsfile_roleFileRolegenexcell_countsglobal_contribution_filtersglobal_contributionsGlobalContributionFiltersGlobalContributionsgroup_keyGroupKeygrowth_statsGrowthStatsgsm_seriesGsmSeriesis_filteredIsFilteredlinked_geolinked_studyLinkedGeoLinkedStudylist_assayslist_countrieslist_organismsListAssaysListCountriesListOrganismsmanifestManifestmatricesMatricesorganism_growthorganism_searchorganism_totalsOrganismGrowthorganismsOrganismsOrganismSearchOrganismTotalspaperPaperprojectProjectproject_citationsproject_enrichedproject_experimentsproject_runsproject_samplesproject_single_cellproject_summaryproject_xrefProjectCitationsProjectEnrichedProjectExperimentsProjectRunsProjectSamplesProjectSingleCellProjectSummaryProjectXrefpublicationsPublicationsqueryQueryquick_annotationQuickAnnotationregister_tablesRegisterTablesresolve_accessionresolve_studyResolveAccessionResolveStudyrunRunsample_bamsample_detailsample_framesample_microbessample_searchSampleBamSampleDetailSampleFrameSampleMicrobesSampleSearchsearch_correctionSearchCorrectionseqout_closeseqout_connectseqout_countsseqout_counts_filesseqout_defaultseqout_matrixseqout_searchseqout_unitsSeqoutCloseSeqoutConnectSeqoutCountsSeqoutCountsFilesSeqoutDefaultSeqoutMatrixSeqoutSearchSeqoutUnitssummariesSummariestablesTables
Dependencies:askpassclicurlDBIgluehttr2lifecyclemagrittropensslpillarpkgconfigR6rlangsystibbleutf8vctrswithr
Getting started with seqout
Last update: 2026-08-16
Started: 2026-03-24
Searching
Filters | Sort order | Converting search results todetailed records | Parquet backend
Last update: 2026-08-16
Started: 2026-08-13
