Bioconductor DuckDB Integration and High-Level I/O

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Documentation for package ‘BiocDuckDB’ version 0.99.22

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

annotateWithRegions-method	MultiAssaySpatialExperiment lazy spatial methods
c-method	DuckDBDualSubset objects
calculateAverage-method	DuckDBMatrix scuttle methods
calculateCPM-method	DuckDBMatrix scuttle methods
calculateTPM-method	DuckDBMatrix scuttle methods
colPair<--method	colPairs/rowPairs setters for DuckDBSelfHits
colPairs<--method	colPairs/rowPairs setters for DuckDBSelfHits
colTable	Sample table methods
colTable-method	Sample table methods
colTable<-	Sample table methods
colTable<--method	Sample table methods
colTableNames	Sample table methods
colTableNames-method	Sample table methods
colTableNames<-	Sample table methods
colTableNames<--method	Sample table methods
colTables	Sample table methods
colTables-method	Sample table methods
colTables<-	Sample table methods
colTables<--method	Sample table methods
correlatePairs-method	DuckDBMatrix scran methods
DuckDBDataFrame-spatial	DuckDBDataFrame spatial methods
DuckDBDualSubset-class	DuckDBDualSubset objects
DuckDBMatrix-scran	DuckDBMatrix scran methods
DuckDBMatrix-scuttle	DuckDBMatrix scuttle methods
findMarkers-method	DuckDBMatrix scran methods
geometricSizeFactors-method	DuckDBMatrix scuttle methods
length-method	DuckDBDualSubset objects
librarySizeFactors-method	DuckDBMatrix scuttle methods
linkSpatialMap	Link assay observations to their spatial layer rows
modelGeneCV2-method	DuckDBMatrix scran methods
modelGeneVar-method	DuckDBMatrix scran methods
modelGeneVarByPoisson-method	DuckDBMatrix scran methods
MultiAssaySpatialExperiment-spatial	MultiAssaySpatialExperiment lazy spatial methods
normalizeCounts-method	DuckDBMatrix scuttle methods
numDetectedAcrossFeatures-method	DuckDBMatrix scuttle methods
pairwiseBinom-method	DuckDBMatrix scran methods
pairwiseTTests-method	DuckDBMatrix scran methods
perCellQCMetrics-method	DuckDBMatrix scuttle methods
perFeatureQCMetrics-method	DuckDBMatrix scuttle methods
readGeoParquetForMASE-method	MultiAssaySpatialExperiment lazy spatial methods
readParquet	Read Parquet Representation of a Bioconductor Object
readParquetForMASE-method	MultiAssaySpatialExperiment lazy spatial methods
rowLoading	Feature loading methods
rowLoading-method	Feature loading methods
rowLoading<-	Feature loading methods
rowLoading<--method	Feature loading methods
rowLoadingNames	Feature loading methods
rowLoadingNames-method	Feature loading methods
rowLoadingNames<-	Feature loading methods
rowLoadingNames<--method	Feature loading methods
rowLoadings	Feature loading methods
rowLoadings-method	Feature loading methods
rowLoadings<-	Feature loading methods
rowLoadings<--method	Feature loading methods
rowPair<--method	colPairs/rowPairs setters for DuckDBSelfHits
rowPairs<--method	colPairs/rowPairs setters for DuckDBSelfHits
rowTable	Feature table methods
rowTable-method	Feature table methods
rowTable<-	Feature table methods
rowTable<--method	Feature table methods
rowTableNames	Feature table methods
rowTableNames-method	Feature table methods
rowTableNames<-	Feature table methods
rowTableNames<--method	Feature table methods
rowTables	Feature table methods
rowTables-method	Feature table methods
rowTables<-	Feature table methods
rowTables<--method	Feature table methods
scoreMarkers-method	DuckDBMatrix scran methods
SingleCellExperiment-colTables	Sample table methods
SingleCellExperiment-loadings	Feature loading methods
SingleCellExperiment-pairs	colPairs/rowPairs setters for DuckDBSelfHits
SingleCellExperiment-rowTables	Feature table methods
spatialCoordinateSystems	Coordinate systems of a MultiAssaySpatialExperiment
spatialElementJoin	Spatial join between a points element and a shapes element of a MASE
spatialJoin-method	DuckDBDataFrame spatial methods
spatialMatch-method	DuckDBDataFrame spatial methods
spatialOverlaps-method	DuckDBDataFrame spatial methods
spatialViews	On-the-fly DuckDB views over a MASE's spatial elements
subsetByBoundingBox-method	MultiAssaySpatialExperiment lazy spatial methods
subsetByPolygon-method	MultiAssaySpatialExperiment lazy spatial methods
sumCountsAcrossFeatures-method	DuckDBMatrix scuttle methods
summarizeAssayByGroup-method	DuckDBMatrix scuttle methods
summaryMarkerStats-method	DuckDBMatrix scran methods
validateSpatialMap	Validate a MASE's spatialMap referential integrity
writeDatapackage	Write a Frictionless datapackage.json envelope
writeParquet	Write Parquet Representation of a Bioconductor Object
writeParquet-method	Write Parquet Representation of a Bioconductor Object
writeStreamingResource	Stream a large table to a single multi-part Parquet resource
[-method	DuckDBDualSubset objects
[<--method	DuckDBDualSubset objects