Introduction | Installation | The round-trip | The storage layout | Advanced: writing and attaching resources directly | Streaming a flat resource from a cursor | Operations run as SQL | Genomic coordinates are preserved | Single-cell data | The filter, realize, analyze pattern | Multi-omics | When to use BiocDuckDB | Session information
Package: BiocDuckDB 0.99.28
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:
BiocDuckDB_0.99.28.tar.gz
BiocDuckDB_0.99.28.zip(r-4.7-any)BiocDuckDB_0.99.28.zip(r-4.6-any)BiocDuckDB_0.99.28.zip(r-4.5-any)
BiocDuckDB_0.99.28.tgz(r-4.6-any)BiocDuckDB_0.99.28.tgz(r-4.5-any)
BiocDuckDB_0.99.28.tar.gz(r-4.7-any)BiocDuckDB_0.99.28.tar.gz(r-4.6-any)
BiocDuckDB_0.99.28.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://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/genentech/biocduckdb/issues
On BioConductor:BiocDuckDB-0.99.26(bioc 3.24)
dataimportdatarepresentationinfrastructurernaseqsequencingsinglecellsoftware
Last updated from:d0fbd4601d. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 316 | ||
| linux-devel | NOTE | 732 | ||
| source / vignettes | OK | 589 | ||
| linux-release | NOTE | 866 | ||
| macos-release | NOTE | 664 | ||
| macos-oldrel | NOTE | 614 | ||
| windows-devel | NOTE | 875 | ||
| windows-release | NOTE | 840 | ||
| windows-oldrel | NOTE | 935 | ||
| wasm-release | OK | 338 |
Exports:annotateWithRegionscalculateAveragecalculateCPMcalculateTPMcolPair<-colPairs<-colTablecolTable<-colTableNamescolTableNames<-colTablescolTables<-correlatePairsDuckDBIrlbaParamfindMarkersgeometricSizeFactorsinitializeCppinitializeOptionslibrarySizeFactorslinkSpatialMaploadIntoMemorymodelGeneCV2modelGeneVarmodelGeneVarByPoissonnormalizeCountsnumDetectedAcrossFeaturespairwiseBinompairwiseTTestsperCellQCMetricsperFeatureQCMetricsreadGeoParquetForMASEreadParquetreadParquetForMASErowLoadingrowLoading<-rowLoadingNamesrowLoadingNames<-rowLoadingsrowLoadings<-rowPair<-rowPairs<-rowTablerowTable<-rowTableNamesrowTableNames<-rowTablesrowTables<-runSVDscoreMarkersspatialCoordinateSystemsspatialElementJoinspatialJoinspatialMatchspatialOverlapsspatialViewssubsetByBoundingBoxsubsetByPolygonsumCountsAcrossFeaturessummarizeAssayByGroupsummaryMarkerStatsvalidateSpatialMapwriteDatapackagewriteParquetwriteStreamingResource
Dependencies:abindarrowaskpassassertthatassortheadbeachmatBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularbitbit64blobblustercachemclassclassIntcliclustercodetoolscpp11curlDBIdbplyrDelayedArraydplyrdqrngduckdbDuckDBArrayDuckDBDataFrameDuckDBGRangese1071edgeRfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2igraphIRangesirlbajsonliteKernSmoothlambda.rlatticelifecyclelimmalocfitmagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemetapodMultiAssayExperimentMultiAssaySpatialExperimentopensslpillarpkgconfigproxypurrrR6RcpprjsonrlangRSQLitersvds2S4ArraysS4VectorsScaledMatrixscranscuttleSeqinfosfSingleCellExperimentsitmosnowSparseArraySpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectunitsutf8vctrswithrwkXVector
Introduction to BiocDuckDB
Last update: 2026-09-30
Started: 2026-07-07
Benchmarking BiocDuckDB
Introduction | What BiocDuckDB optimizes | A small, live comparison | Benchmark setup | Results | Summary | When this matters | Running your own benchmarks | Session information
Last update: 2026-09-11
Started: 2026-07-07
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DuckDBDataFrame spatial methods | DuckDBDataFrame-spatial spatialJoin,DataFrame,DuckDBDataFrame-method spatialJoin,DuckDBDataFrame,DataFrame-method spatialJoin,DuckDBDataFrame,DuckDBDataFrame-method spatialJoin,DuckDBDataFrame,sf-method spatialJoin,sf,DuckDBDataFrame-method spatialMatch,DuckDBDataFrame,DataFrame-method spatialMatch,DuckDBDataFrame,DuckDBDataFrame-method spatialMatch,DuckDBDataFrame,sf-method spatialOverlaps,DuckDBDataFrame-method |
| DuckDBDualSubset objects | c,DuckDBDualSubset-method DuckDBDualSubset-class length,DuckDBDualSubset-method [,DuckDBDualSubset,ANY,ANY,ANY-method [<-,DuckDBDualSubset,ANY,ANY,ANY-method |
| A fast SVD path for DuckDB-backed matrices | DuckDBIrlbaParam DuckDBIrlbaParam-class runSVD,DuckDBIrlbaParam-method |
| DuckDBMatrix scran methods | correlatePairs,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 methods | calculateAverage,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 |
| Initialize DuckDB-backed matrices for beachmat | initializeCpp initializeCpp,DuckDBArraySeed-method |
| Options for DuckDB-backed matrices | initializeOptions |
| Link assay observations to their spatial layer rows | linkSpatialMap |
| Load a DuckDB-backed matrix into memory | loadIntoMemory |
| MultiAssaySpatialExperiment lazy spatial methods | annotateWithRegions,MultiAssaySpatialExperiment-method MultiAssaySpatialExperiment-spatial readGeoParquetForMASE,character-method readParquetForMASE,character-method subsetByBoundingBox,MultiAssaySpatialExperiment-method subsetByPolygon,MultiAssaySpatialExperiment-method |
| Read Parquet Representation of a Bioconductor Object | readParquet |
| Sample table methods | colTable 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 methods | rowLoading 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 DuckDBSelfHits | colPair<-,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 methods | rowTable 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 MultiAssaySpatialExperiment | spatialCoordinateSystems |
| Spatial join between a points element and a shapes element of a MASE | spatialElementJoin |
| On-the-fly DuckDB views over a MASE's spatial elements | spatialViews |
| Validate a MASE's spatialMap referential integrity | validateSpatialMap |
| Write a Frictionless datapackage.json envelope | writeDatapackage |
| Write Parquet Representation of a Bioconductor Object | writeParquet 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 |
| Stream a large table to a single multi-part Parquet resource | writeStreamingResource |