Package: DuckDBDataFrame 0.99.6

Patrick Aboyoun

DuckDBDataFrame: DuckDB-Backed DataFrame and Table Structures

Provides DuckDB-backed implementations of core tabular data structures including DuckDBTable, DuckDBDataFrame, and DuckDBColumn. These classes extend Bioconductor's S4Vectors framework to enable efficient, out-of-memory operations on large tabular datasets using DuckDB's analytical database engine. The package includes SQL function discovery, connection management, and support for list columns and embeddings stored in ARRAY[] columns.

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

DuckDBDataFrame_0.99.6.tar.gz
DuckDBDataFrame_0.99.6.zip(r-4.7-any)DuckDBDataFrame_0.99.6.zip(r-4.6-any)DuckDBDataFrame_0.99.6.zip(r-4.5-any)
DuckDBDataFrame_0.99.6.tgz(r-4.6-any)DuckDBDataFrame_0.99.6.tgz(r-4.5-any)
DuckDBDataFrame_0.99.6.tar.gz(r-4.7-any)DuckDBDataFrame_0.99.6.tar.gz(r-4.6-any)
DuckDBDataFrame_0.99.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DuckDBDataFrame/json (API)

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

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

On CRAN:

Conda:

dataimportdatarepresentationinfrastructuresoftware

5.31 score 4 packages 115 exports 40 dependencies

Last updated from:62ef6ff1b4. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING192
linux-devel-x86_64NOTE355
source / vignettesOK267
linux-release-x86_64NOTE311
macos-release-arm64NOTE261
macos-oldrel-arm64NOTE213
windows-devel-x86_64NOTE306
windows-release-x86_64NOTE304
windows-oldrel-x86_64NOTE286
wasm-releaseOK126

Exports:.has_row_number.keycols.makePrettyCharacterMatrixForDisplay.set_row_number%in%acquireDuckDBConnarrowIntTypearrowTypearrowTypeFromNamearrowTypeToNameas.data.frameas.envas.listbindCOLSbindROWSbuildParquetCopySQLcbindchartrcheckAppendPartcheckHiveAppendPartitionsclusterSortcolnamescolnames<-coltypescoltypes<-columnMetadatacolumnMetadata<-commonColnamesconfigureCloudconfigureOutOfCorecountLnodeHitscountRnodeHitsdbconndimtblsdimtbls<-DuckDBDataFrameDuckDBSelfHitsDuckDBTableelementMetadataelementMetadata<-elementNROWSendsWithescapeSQLPathextractCOLSextractNODESextractROWSfromgetListElementgreplgsubheadhilbertIQRis_nonzerois_sparsekeydimnameskeydimnames<-keynamesloadExtensionmadmakeNakedCharacterMatrixForDisplayMathmeanncharncolncolsnkeynkeydimnormalizeSingleBracketReplacementValuenrownzcountOpsparquetPartPathpastepaste2pmaxpminquoteSQLColumnsreadParquetSchemarealizereconcileParquetSchemareleaseDuckDBConnreplaceCOLSreplaceROWSrownamesrownames<-sdsetupFlatParquetWriteshowshowAsCellsplitsql_callsql_funstartsWithsubsubsetsubstrsubstringSummarytt.DuckDBDataFrametabletailtblconntotolowertouppertypetype<-uniquevalidateAppendOffsetvalidateWriteParquetPartvarwriteDuckDBTableParquetzorder

Dependencies:abindarrowassertthatBiocGenericsbitbit64blobclicpp11DBIdbplyrDelayedArraydplyrduckdbgenericsglueIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpurrrR6rlangS4ArraysS4VectorsSparseArraystringistringrtibbletidyrtidyselectutf8vctrswithrXVector

Introduction to DuckDBDataFrame
Introduction | Installation | Quick start | Working with a DuckDBDataFrame | Column access | Row subsetting | Computed columns | Column metadata | Columns come in three flavors | Reaching for SQL directly | When to use DuckDBDataFrame | Session information
Rendered fromDuckDBDataFrame.Rmdusingknitr::rmarkdown

Last update: 2026-07-06
Started: 2026-07-06

Design and extension of DuckDBDataFrame
Scope | The classes | The DuckDBTable abstraction | Construction | The contract | Key-dimension semantics | From R to SQL | Connection management | Dimension tables | Extending DuckDBDataFrame | Session information
Rendered fromDuckDBDataFrame-design.Rmdusingknitr::rmarkdown

Last update: 2026-07-06
Started: 2026-07-06

Readme and manuals

Help Manual

Help pageTopics
Arrow type helpers for the DuckDB package suitearrow-types arrowIntType arrowType arrowTypeFromName arrowTypeToName
DuckDBAtomicList objectsas.list,DuckDBAtomicList-method DuckDBAtomicList-class DuckDBCharacterList-class DuckDBFactorList-class DuckDBInteger64List-class DuckDBIntegerList-class DuckDBLogicalList-class DuckDBNumericList-class elementNROWS,DuckDBAtomicList-method extractROWS,DuckDBAtomicList,ANY-method getListElement,DuckDBAtomicList-method head,DuckDBAtomicList-method realize,DuckDBAtomicList-method show,DuckDBAtomicList-method showAsCell,DuckDBAtomicList-method tail,DuckDBAtomicList-method
DuckDBColumn objects.has_row_number,DuckDBColumn-method .keycols,DuckDBColumn-method as.vector,DuckDBColumn-method dbconn,DuckDBColumn-method dimtbls,DuckDBColumn-method dimtbls<-,DuckDBColumn-method DuckDBColumn-class extractROWS,DuckDBColumn,ANY-method head,DuckDBColumn-method length,DuckDBColumn-method names,DuckDBColumn-method names<-,DuckDBColumn-method realize,DuckDBColumn-method show,DuckDBColumn-method showAsCell,DuckDBColumn-method tail,DuckDBColumn-method tblconn,DuckDBColumn-method type,DuckDBColumn-method type<-,DuckDBColumn-method
Common operations on DuckDBColumn objects!,DuckDBColumn-method %in%,DuckDBColumn,ANY-method chartr,ANY,ANY,DuckDBColumn-method DuckDBColumn-utils endsWith,DuckDBColumn-method grepl,ANY,DuckDBColumn-method gsub,ANY,ANY,DuckDBColumn-method IQR,DuckDBColumn-method is.finite,DuckDBColumn-method is.infinite,DuckDBColumn-method is.nan,DuckDBColumn-method is_nonzero,DuckDBColumn-method mad,DuckDBColumn-method Math,DuckDBColumn-method mean,DuckDBColumn-method median.DuckDBColumn nchar,DuckDBColumn-method nzcount,DuckDBColumn-method Ops,atomic,DuckDBColumn-method Ops,DuckDBColumn,atomic-method Ops,DuckDBColumn,DuckDBColumn-method Ops,DuckDBColumn,missing-method paste,DuckDBColumn-method paste2,character,DuckDBColumn-method paste2,DuckDBColumn,character-method paste2,DuckDBColumn,DuckDBColumn-method pmax,DuckDBColumn-method pmin,DuckDBColumn-method quantile.DuckDBColumn sd,DuckDBColumn-method sql_call,DuckDBColumn-method sql_fun,DuckDBColumn-method startsWith,DuckDBColumn-method sub,ANY,ANY,DuckDBColumn-method substr,DuckDBColumn-method substring,DuckDBColumn-method Summary,DuckDBColumn-method table,DuckDBColumn-method tolower,DuckDBColumn-method toupper,DuckDBColumn-method unique,DuckDBColumn-method var,DuckDBColumn,ANY-method
Acquire and Release the DuckDB ConnectionacquireDuckDBConn configureCloud configureOutOfCore DuckDBConnection loadExtension releaseDuckDBConn
DuckDBDataFrame objects.makePrettyCharacterMatrixForDisplay as.data.frame,DuckDBDataFrame-method as.matrix,DuckDBDataFrame-method cbind,DuckDBDataFrame-method cbind.DuckDBDataFrame coerce,DuckDBDataFrame,DFrame-method colnames<-,DuckDBDataFrame-method DuckDBDataFrame DuckDBDataFrame-class length,DuckDBDataFrame-method makeNakedCharacterMatrixForDisplay,DuckDBDataFrame-method names,DuckDBDataFrame-method names<-,DuckDBDataFrame-method normalizeSingleBracketReplacementValue,DuckDBDataFrame-method realize,DuckDBDataFrame-method replaceCOLS,DuckDBDataFrame-method replaceROWS,DuckDBDataFrame-method rownames<-,DuckDBDataFrame-method show,DuckDBDataFrame-method subset,DuckDBDataFrame-method [,DuckDBDataFrame,ANY,ANY,ANY-method [[,DuckDBDataFrame-method [[<-,DuckDBDataFrame-method
DuckDBDataFrameList objectscoerce,DuckDBDataFrameList,DFrameList-method colnames<-,DuckDBDataFrameList-method columnMetadata,DuckDBDataFrameList-method columnMetadata<-,DuckDBDataFrameList-method commonColnames,DuckDBDataFrameList-method dbconn,DuckDBDataFrameList-method dimtbls,DuckDBDataFrameList-method dimtbls<-,DuckDBDataFrameList-method DuckDBDataFrameList-class elementNROWS,DuckDBDataFrameList-method extractROWS,DuckDBDataFrameList,ANY-method getListElement,DuckDBDataFrameList-method head,DuckDBDataFrameList-method length,DuckDBDataFrameList-method names,DuckDBDataFrameList-method names<-,DuckDBDataFrameList-method ncols,DuckDBDataFrameList-method realize,DuckDBDataFrameList-method rownames<-,DuckDBDataFrameList-method split,DuckDBDataFrame,DuckDBColumn-method tail,DuckDBDataFrameList-method tblconn,DuckDBDataFrameList-method unlist,DuckDBDataFrameList-method
DuckDBEmbeddings objectsas.list,DuckDBEmbeddings-method as.matrix,DuckDBEmbeddings-method colnames,DuckDBEmbeddings-method colnames<-,DuckDBEmbeddings-method DuckDBEmbeddings-class extractCOLS,DuckDBEmbeddings-method ncol,DuckDBEmbeddings-method nrow,DuckDBEmbeddings-method realize,DuckDBEmbeddings-method rownames,DuckDBEmbeddings-method rownames<-,DuckDBEmbeddings-method show,DuckDBEmbeddings-method showAsCell,DuckDBEmbeddings-method [,DuckDBEmbeddings,ANY,ANY,ANY-method
DuckDBSelfHits objects.has_row_number,DuckDBSelfHits-method .keycols,DuckDBSelfHits-method as.data.frame,DuckDBSelfHits-method coerce,DuckDBSelfHits,DFrame-method coerce,DuckDBSelfHits,dgCMatrix-method coerce,DuckDBSelfHits,DuckDBDataFrame-method countLnodeHits,DuckDBSelfHits-method countRnodeHits,DuckDBSelfHits-method dbconn,DuckDBSelfHits-method dimtbls,DuckDBSelfHits-method dimtbls<-,DuckDBSelfHits-method DuckDBSelfHits DuckDBSelfHits-class elementMetadata,DuckDBSelfHits-method elementMetadata<-,DuckDBSelfHits-method extractNODES extractNODES,DuckDBSelfHits-method extractROWS,DuckDBSelfHits,ANY-method from,DuckDBSelfHits-method head,DuckDBSelfHits-method length,DuckDBSelfHits-method realize,DuckDBSelfHits-method show,DuckDBSelfHits-method tail,DuckDBSelfHits-method tblconn,DuckDBSelfHits-method to,DuckDBSelfHits-method [,DuckDBSelfHits,ANY,ANY,ANY-method
DuckDBTable objects.has_row_number .has_row_number,DuckDBTable-method .keycols .keycols,DuckDBTable-method .set_row_number all.equal.DuckDBTable as.data.frame,DuckDBTable-method as.env,DuckDBTable-method bindCOLS,DuckDBTable-method bindROWS,DuckDBTable-method colnames,DuckDBTable-method colnames<-,DuckDBTable-method coltypes coltypes,DuckDBTable-method coltypes<- coltypes<-,DuckDBTable-method dbconn,DuckDBTable-method dimtbls dimtbls,DuckDBTable-method dimtbls<- dimtbls<-,DuckDBTable-method DuckDBTable DuckDBTable-class extractCOLS,DuckDBTable-method extractROWS,DuckDBTable,ANY-method head,DuckDBTable-method ncol,DuckDBTable-method nrow,DuckDBTable-method rownames,DuckDBTable-method show,DuckDBTable-method subset,DuckDBTable-method tail,DuckDBTable-method tblconn,DuckDBTable-method [,DuckDBTable,ANY,ANY,ANY-method
Common operations on DuckDBTable objects!,DuckDBTable-method %in%,DuckDBTable,ANY-method chartr,ANY,ANY,DuckDBTable-method DuckDBTable-utils elementNROWS,DuckDBTable-method endsWith,DuckDBTable-method grepl,ANY,DuckDBTable-method gsub,ANY,ANY,DuckDBTable-method IQR,DuckDBTable-method is.finite,DuckDBTable-method is.infinite,DuckDBTable-method is.nan,DuckDBTable-method is_nonzero,DuckDBTable-method is_sparse,DuckDBTable-method mad,DuckDBTable-method Math,DuckDBTable-method mean,DuckDBTable-method median.DuckDBTable nchar,DuckDBTable-method nzcount,DuckDBTable-method Ops,atomic,DuckDBTable-method Ops,DuckDBTable,atomic-method Ops,DuckDBTable,DuckDBTable-method Ops,DuckDBTable,missing-method paste,DuckDBTable-method paste2,character,DuckDBTable-method paste2,DuckDBTable,character-method paste2,DuckDBTable,DuckDBTable-method pmax,DuckDBTable-method pmin,DuckDBTable-method quantile.DuckDBTable sd,DuckDBTable-method sql_call,DuckDBTable-method sql_fun,DuckDBTable-method startsWith,DuckDBTable-method sub,ANY,ANY,DuckDBTable-method substr,DuckDBTable-method substring,DuckDBTable-method Summary,DuckDBTable-method table,DuckDBTable-method tolower,DuckDBTable-method toupper,DuckDBTable-method unique,DuckDBTable-method var,DuckDBTable,ANY-method
DuckDBTransposedDataFrame objectsas.matrix,DuckDBTransposedDataFrame-method dbconn,DuckDBTransposedDataFrame-method dimtbls,DuckDBTransposedDataFrame-method dimtbls<-,DuckDBTransposedDataFrame-method DuckDBTransposedDataFrame-class realize,DuckDBTransposedDataFrame-method show,DuckDBTransposedDataFrame-method t,DuckDBDataFrame-method t.DuckDBDataFrame tblconn,DuckDBTransposedDataFrame-method
Key Names and Key Countkeydimnames keydimnames,DuckDBTable-method keydimnames<- keydimnames<-,DuckDBTable-method keynames keynames,DuckDBTable-method nkey nkey,DuckDBTable-method nkeydim nkeydim,DuckDBTable-method
Cluster-on-write keys and helpersclusterSort hilbert parquet-io-cluster zorder
Call DuckDB SQL Functions on BiocDuckDB Objectssql_call
Find Compatible DuckDB SQL Functions for BiocDuckDB Objectssql_fun
Accessing DB Table Informationtblconn