Package: BiocDuckDB 0.99.5

Patrick Aboyoun

BiocDuckDB: Bioconductor DuckDB Integration and High-Level I/O

Integration package providing high-level Parquet I/O functions and optimized methods for single-cell analysis workflows using DuckDB-backed data structures. Includes readParquet and writeParquet functions for seamless serialization of SummarizedExperiment, SingleCellExperiment, MultiAssayExperiment, and MultiAssaySpatialExperiment objects, plus SQL-optimized implementations of scran and scuttle methods for variance modeling, marker detection, QC metrics, and normalization. This package brings together DuckDBDataFrame, DuckDBArray, DuckDBGRanges, and DuckDBSpatial (optional) for complete Bioconductor integration.

Authors:Patrick Aboyoun [aut, cre], Genentech, Inc. [cph]

BiocDuckDB_0.99.5.tar.gz
BiocDuckDB_0.99.5.zip(r-4.7-any)BiocDuckDB_0.99.5.zip(r-4.6-any)BiocDuckDB_0.99.5.zip(r-4.5-any)
BiocDuckDB_0.99.5.tgz(r-4.6-any)BiocDuckDB_0.99.5.tgz(r-4.5-any)
BiocDuckDB_0.99.5.tar.gz(r-4.7-any)BiocDuckDB_0.99.5.tar.gz(r-4.6-any)
BiocDuckDB_0.99.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BiocDuckDB/json (API)

# Install 'BiocDuckDB' in R:
install.packages('BiocDuckDB', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biocstaging/biocduckdb/issues

On CRAN:

Conda:

dataimportdatarepresentationinfrastructurernaseqsequencingsinglecellsoftware

4.30 score 58 exports 104 dependencies

Last updated from:17137e0aca. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING349
linux-devel-x86_64NOTE552
source / vignettesOK446
linux-release-x86_64NOTE648
macos-release-arm64NOTE313
macos-oldrel-arm64NOTE514
windows-devel-x86_64NOTE963
windows-release-x86_64NOTE978
windows-oldrel-x86_64NOTE998
wasm-releaseOK273

Exports:annotateWithRegionscalculateAveragecalculateCPMcalculateTPMcolPair<-colPairs<-colTablecolTable<-colTableNamescolTableNames<-colTablescolTables<-correlatePairsfindMarkersgeometricSizeFactorslibrarySizeFactorslinkSpatialMapmodelGeneCV2modelGeneVarmodelGeneVarByPoissonnormalizeCountsnumDetectedAcrossFeaturespairwiseBinompairwiseTTestsperCellQCMetricsperFeatureQCMetricsreadGeoParquetForMASEreadParquetreadParquetForMASErowLoadingrowLoading<-rowLoadingNamesrowLoadingNames<-rowLoadingsrowLoadings<-rowPair<-rowPairs<-rowTablerowTable<-rowTableNamesrowTableNames<-rowTablesrowTables<-scoreMarkersspatialCoordinateSystemsspatialElementJoinspatialJoinspatialMatchspatialOverlapsspatialViewssubsetByBoundingBoxsubsetByPolygonsumCountsAcrossFeaturessummarizeAssayByGroupsummaryMarkerStatsvalidateSpatialMapwriteDatapackagewriteParquet

Dependencies:abindarrowaskpassassertthatassortheadbeachmatBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularbitbit64blobblustercachemclassclassIntcliclustercodetoolscpp11curlDBIdbplyrDelayedArraydplyrdqrngduckdbDuckDBArrayDuckDBDataFrameDuckDBGRangese1071edgeRfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2igraphIRangesirlbajsonliteKernSmoothlambda.rlatticelifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodMultiAssayExperimentMultiAssaySpatialExperimentopensslpillarpkgconfigproxypurrrR6RcpprjsonrlangRSQLitersvds2S4ArraysS4VectorsScaledMatrixscranscuttleSeqinfosfSingleCellExperimentsitmosnowSparseArraySpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectunitsutf8vctrswithrwkXVector

Introduction to BiocDuckDB
Introduction | Installation | The round-trip | The storage layout | Targeting the storage contract | Operations run as SQL | Genomic coordinates are preserved | Single-cell data | The filter, realize, analyze pattern | Multi-omics | When to use BiocDuckDB | Session information
Rendered fromBiocDuckDB.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2026-07-07

Benchmarking BiocDuckDB
Introduction | What BiocDuckDB optimizes | A small, live comparison | Benchmark setup | Results | Main takeaways | When this matters | Running your own benchmarks | Session information
Rendered fromBiocDuckDB-benchmark.Rmdusingknitr::rmarkdown

Last update: 2026-07-07
Started: 2026-07-07

Readme and manuals

Help Manual

Help pageTopics
DuckDBDataFrame spatial methodsDuckDBDataFrame-spatial spatialJoin,DuckDBDataFrame,DuckDBDataFrame-method spatialMatch,DuckDBDataFrame,DataFrame-method spatialMatch,DuckDBDataFrame,DuckDBDataFrame-method spatialOverlaps,DuckDBDataFrame-method
DuckDBDualSubset objectsc,DuckDBDualSubset-method DuckDBDualSubset-class length,DuckDBDualSubset-method [,DuckDBDualSubset,ANY,ANY,ANY-method [<-,DuckDBDualSubset,ANY,ANY,ANY-method
DuckDBMatrix scran methodscorrelatePairs,DuckDBMatrix-method DuckDBMatrix-scran findMarkers,DuckDBMatrix-method modelGeneCV2,DuckDBMatrix-method modelGeneVar,DuckDBMatrix-method modelGeneVarByPoisson,DuckDBMatrix-method pairwiseBinom,DuckDBMatrix-method pairwiseTTests,DuckDBMatrix-method scoreMarkers,DuckDBMatrix-method summaryMarkerStats,DuckDBMatrix-method
DuckDBMatrix scuttle methodscalculateAverage,DuckDBMatrix-method calculateCPM,DuckDBMatrix-method calculateTPM,DuckDBMatrix-method DuckDBMatrix-scuttle geometricSizeFactors,DuckDBMatrix-method librarySizeFactors,DuckDBMatrix-method normalizeCounts,DuckDBMatrix-method numDetectedAcrossFeatures,DuckDBMatrix-method perCellQCMetrics,DuckDBMatrix-method perFeatureQCMetrics,DuckDBMatrix-method sumCountsAcrossFeatures,DuckDBMatrix-method summarizeAssayByGroup,DuckDBMatrix-method
Link assay observations to their spatial layer rowslinkSpatialMap
MultiAssaySpatialExperiment lazy spatial methodsannotateWithRegions,MultiAssaySpatialExperiment-method MultiAssaySpatialExperiment-spatial readGeoParquetForMASE,character-method readParquetForMASE,character-method subsetByBoundingBox,MultiAssaySpatialExperiment-method subsetByPolygon,MultiAssaySpatialExperiment-method
Read Parquet Representation of a Bioconductor ObjectreadParquet
Sample table methodscolTable colTable,SingleCellExperiment,character-method colTable,SingleCellExperiment,missing-method colTable,SingleCellExperiment,numeric-method colTable<- colTable<-,SingleCellExperiment,character-method colTable<-,SingleCellExperiment,missing-method colTable<-,SingleCellExperiment,numeric-method colTableNames colTableNames,SingleCellExperiment-method colTableNames<- colTableNames<-,SingleCellExperiment,character-method colTables colTables,SingleCellExperiment-method colTables<- colTables<-,SingleCellExperiment-method SingleCellExperiment-colTables
Feature loading methodsrowLoading rowLoading,SingleCellExperiment,character-method rowLoading,SingleCellExperiment,missing-method rowLoading,SingleCellExperiment,numeric-method rowLoading<- rowLoading<-,SingleCellExperiment,character-method rowLoading<-,SingleCellExperiment,missing-method rowLoading<-,SingleCellExperiment,numeric-method rowLoadingNames rowLoadingNames,SingleCellExperiment-method rowLoadingNames<- rowLoadingNames<-,SingleCellExperiment,character-method rowLoadings rowLoadings,SingleCellExperiment-method rowLoadings<- rowLoadings<-,SingleCellExperiment-method SingleCellExperiment-loadings
colPairs/rowPairs setters for DuckDBSelfHitscolPair<-,SingleCellExperiment,character,DuckDBSelfHits-method colPair<-,SingleCellExperiment,missing,DuckDBSelfHits-method colPair<-,SingleCellExperiment,numeric,DuckDBSelfHits-method colPairs<-,SingleCellExperiment,DuckDBSelfHits-method rowPair<-,SingleCellExperiment,character,DuckDBSelfHits-method rowPair<-,SingleCellExperiment,missing,DuckDBSelfHits-method rowPair<-,SingleCellExperiment,numeric,DuckDBSelfHits-method rowPairs<-,SingleCellExperiment,DuckDBSelfHits-method SingleCellExperiment-pairs
Feature table methodsrowTable rowTable,SingleCellExperiment,character-method rowTable,SingleCellExperiment,missing-method rowTable,SingleCellExperiment,numeric-method rowTable<- rowTable<-,SingleCellExperiment,character-method rowTable<-,SingleCellExperiment,missing-method rowTable<-,SingleCellExperiment,numeric-method rowTableNames rowTableNames,SingleCellExperiment-method rowTableNames<- rowTableNames<-,SingleCellExperiment,character-method rowTables rowTables,SingleCellExperiment-method rowTables<- rowTables<-,SingleCellExperiment-method SingleCellExperiment-rowTables
Coordinate systems of a MultiAssaySpatialExperimentspatialCoordinateSystems
Spatial join between two elements of a MASEspatialElementJoin
On-the-fly DuckDB views over a MASE's spatial elementsspatialViews
Validate a MASE's spatialMap referential integrityvalidateSpatialMap
Write a Frictionless datapackage.json envelopewriteDatapackage
Write Parquet Representation of a Bioconductor ObjectwriteParquet writeParquet,ANY-method writeParquet,Assays-method writeParquet,data.frame-method writeParquet,DataFrame-method writeParquet,DuckDBDataFrame-method writeParquet,DuckDBGRanges-method writeParquet,DuckDBGRangesList-method writeParquet,DuckDBSelfHits-method writeParquet,DuckDBTable-method writeParquet,DuckDBTransposedDataFrame-method writeParquet,ExperimentList-method writeParquet,GenomicRanges-method writeParquet,GenomicRangesList-method writeParquet,List-method writeParquet,list-method writeParquet,MultiAssayExperiment-method writeParquet,MultiAssaySpatialExperiment-method writeParquet,PointsLayerList-method writeParquet,SelfHits-method writeParquet,ShapesLayerList-method writeParquet,SingleCellExperiment-method writeParquet,SummarizedExperiment-method writeParquet,TransposedDataFrame-method