Package: DuckDBGRanges 0.99.8

Patrick Aboyoun

DuckDBGRanges: DuckDB-Backed GenomicRanges Implementation

Provides DuckDB-backed implementations of GenomicRanges data structures for efficient, out-of-memory operations on large genomic interval datasets. The package includes DuckDBGRanges and DuckDBGRangesList classes with optimized range operations including restrict, flank, shift, findOverlaps, coverage, and distance calculations. Ideal for variant analysis, scATAC-seq peak analysis, and other genomic workflows requiring memory-efficient range operations on large datasets.

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

DuckDBGRanges_0.99.8.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DuckDBGRanges/json (API)

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

Bug tracker:https://github.com/genentech/duckdbgranges/issues

On BioConductor:DuckDBGRanges-0.99.8(bioc 3.24)

dataimportdatarepresentationinfrastructuresequencingsoftware

5.83 score 1 packages 8 scripts 200 downloads 67 exports 43 dependencies

Last updated from:86c1be7bda. Checks:8 NOTE, 2 OK. Indexed: yes.

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bioc-checksNOTE211
linux-develNOTE670
source / vignettesOK331
linux-releaseNOTE537
macos-releaseNOTE388
macos-oldrelNOTE409
windows-develNOTE841
windows-releaseNOTE899
windows-oldrelNOTE813
wasm-releaseOK195

Exports:as.data.framecoercecountOverlapscoveragedbconndimtblsdimtbls<-disjoindistancedistanceToNearestDuckDBGRangesDuckDBGRangesListduplicatedelementMetadataelementMetadata<-elementNROWSendextractROWSfindOverlapsflankfollowgapsgenome<-getListElementhas_row_numberheadintersectis.unsortedkeycolsmatchnarrownearestorderoverlapsAnypgappintersectprecedepromoterspsetdiffpunionrangesrankrealizereduceresizerestrictseqinfoseqlengths<-seqnamessetdiffshiftshowslidingWindowssortsplitstartstrandsubsetByOverlapstailtblconnterminatorstiletrimunionuniqueupdateObjectwidth

Dependencies:abindarrowassertthatBiocGenericsbitbit64blobclicpp11DBIdbplyrDelayedArraydplyrduckdbDuckDBDataFramegenericsGenomicRangesglueIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpurrrR6rlangS4ArraysS4VectorsSeqinfoSparseArraystringistringrtibbletidyrtidyselectutf8vctrswithrXVector

Benchmarking DuckDBGRanges
Introduction | What DuckDBGRanges optimizes | A small, live comparison | Benchmark setup | Results | Summary | Backend comparison | When to use each | Running your own benchmarks | Session information
Rendered fromDuckDBGRanges-benchmark.Rmdusingknitr::rmarkdown

Last update: 2026-09-03
Started: 2026-07-06

Introduction to DuckDBGRanges
Introduction | Installation | Quick start | Working with a DuckDBGRanges | Accessors | Subsetting | Range operations | Filter, then materialize | Grouped ranges: DuckDBGRangesList | When to use DuckDBGRanges | Session information
Rendered fromDuckDBGRanges.Rmdusingknitr::rmarkdown

Last update: 2026-08-20
Started: 2026-07-06

Design and extension of DuckDBGRanges
Scope | Architecture | Slots | The five required columns | From range operations to SQL | Grouped ranges as LIST columns | Materialization and interoperability | Session information
Rendered fromDuckDBGRanges-design.Rmdusingknitr::rmarkdown

Last update: 2026-08-05
Started: 2026-07-06

Readme and manuals

Help Manual

Help pageTopics
DuckDBGRanges objectsas.data.frame,DuckDBGRanges-method coerce,DuckDBGRanges,DuckDBDataFrame-method coerce,DuckDBGRanges,GRanges-method dbconn,DuckDBGRanges-method dimtbls,DuckDBGRanges-method dimtbls<-,DuckDBGRanges-method DuckDBGRanges DuckDBGRanges-class elementMetadata,DuckDBGRanges-method elementMetadata<-,DuckDBGRanges-method end,DuckDBGRanges-method extractROWS,DuckDBGRanges,ANY-method genome<-,DuckDBGRanges-method has_row_number,DuckDBGRanges-method head,DuckDBGRanges-method keycols,DuckDBGRanges-method length,DuckDBGRanges-method names,DuckDBGRanges-method ranges,DuckDBGRanges-method realize,DuckDBGRanges-method seqinfo,DuckDBGRanges-method seqlengths<-,DuckDBGRanges-method seqnames,DuckDBGRanges-method show,DuckDBGRanges-method start,DuckDBGRanges-method strand,DuckDBGRanges-method tail,DuckDBGRanges-method tblconn,DuckDBGRanges-method width,DuckDBGRanges-method [,DuckDBGRanges,ANY,ANY,ANY-method
Utilities for DuckDBGRanges objectscountOverlaps,DuckDBGRanges,DuckDBGRanges-method countOverlaps,DuckDBGRanges,GRanges-method countOverlaps,GRanges,DuckDBGRanges-method coverage,DuckDBGRanges-method disjoin,DuckDBGRanges-method distance,DuckDBGRanges,DuckDBGRanges-method distance,DuckDBGRanges,GRanges-method distance,GRanges,DuckDBGRanges-method distanceToNearest,DuckDBGRanges,DuckDBGRanges-method distanceToNearest,DuckDBGRanges,GRanges-method distanceToNearest,DuckDBGRanges,missing-method distanceToNearest,GRanges,DuckDBGRanges-method DuckDBGRanges-utils duplicated,DuckDBGRanges-method findOverlaps,DuckDBGRanges,DuckDBGRanges-method findOverlaps,DuckDBGRanges,GRanges-method findOverlaps,GRanges,DuckDBGRanges-method flank,DuckDBGRanges-method follow,DuckDBGRanges,DuckDBGRanges-method follow,DuckDBGRanges,GRanges-method follow,DuckDBGRanges,missing-method follow,GRanges,DuckDBGRanges-method gaps,DuckDBGRanges-method intersect,DuckDBGRanges,DuckDBGRanges-method intersect,DuckDBGRanges,GRanges-method intersect,GRanges,DuckDBGRanges-method is.unsorted,DuckDBGRanges-method match,DuckDBGRanges,DuckDBGRanges-method narrow,DuckDBGRanges-method nearest,DuckDBGRanges,DuckDBGRanges-method nearest,DuckDBGRanges,GRanges-method nearest,DuckDBGRanges,missing-method nearest,GRanges,DuckDBGRanges-method order,DuckDBGRanges-method overlapsAny,DuckDBGRanges,DuckDBGRanges-method overlapsAny,DuckDBGRanges,GRanges-method overlapsAny,GRanges,DuckDBGRanges-method pgap,DuckDBGRanges,DuckDBGRanges-method pgap,DuckDBGRanges,GRanges-method pgap,GRanges,DuckDBGRanges-method pintersect,DuckDBGRanges,DuckDBGRanges-method pintersect,DuckDBGRanges,GRanges-method pintersect,GRanges,DuckDBGRanges-method precede,DuckDBGRanges,DuckDBGRanges-method precede,DuckDBGRanges,GRanges-method precede,DuckDBGRanges,missing-method precede,GRanges,DuckDBGRanges-method promoters,DuckDBGRanges-method psetdiff,DuckDBGRanges,DuckDBGRanges-method psetdiff,DuckDBGRanges,GRanges-method psetdiff,GRanges,DuckDBGRanges-method punion,DuckDBGRanges,DuckDBGRanges-method punion,DuckDBGRanges,GRanges-method punion,GRanges,DuckDBGRanges-method range,DuckDBGRanges-method rank,DuckDBGRanges-method reduce,DuckDBGRanges-method resize,DuckDBGRanges-method restrict,DuckDBGRanges-method setdiff,DuckDBGRanges,DuckDBGRanges-method setdiff,DuckDBGRanges,GRanges-method setdiff,GRanges,DuckDBGRanges-method shift,DuckDBGRanges-method slidingWindows,DuckDBGRanges-method sort,DuckDBGRanges-method subsetByOverlaps,DuckDBGRanges,DuckDBGRanges-method subsetByOverlaps,DuckDBGRanges,GRanges-method terminators,DuckDBGRanges-method tile,DuckDBGRanges-method trim,DuckDBGRanges-method union,DuckDBGRanges,DuckDBGRanges-method union,DuckDBGRanges,GRanges-method union,GRanges,DuckDBGRanges-method unique,DuckDBGRanges-method
DuckDBGRangesList objectscoerce,DuckDBGRangesList,CompressedGRangesList-method coerce,DuckDBGRangesList,DuckDBDataFrame-method dbconn,DuckDBGRangesList-method dimtbls,DuckDBGRangesList-method dimtbls<-,DuckDBGRangesList-method DuckDBGRangesList DuckDBGRangesList-class elementMetadata,DuckDBGRangesList-method elementMetadata<-,DuckDBGRangesList-method elementNROWS,DuckDBGRangesList-method end,DuckDBGRangesList-method extractROWS,DuckDBGRangesList,ANY-method genome<-,DuckDBGRangesList-method getListElement,DuckDBGRangesList-method has_row_number,DuckDBGRangesList-method head,DuckDBGRangesList-method keycols,DuckDBGRangesList-method length,DuckDBGRangesList-method names,DuckDBGRangesList-method names<-,DuckDBGRangesList-method realize,DuckDBGRangesList-method seqinfo,DuckDBGRangesList-method seqlengths<-,DuckDBGRangesList-method seqnames,DuckDBGRangesList-method show,DuckDBGRangesList-method split,DuckDBGRanges,DuckDBColumn-method start,DuckDBGRangesList-method strand,DuckDBGRangesList-method tail,DuckDBGRangesList-method tblconn,DuckDBGRangesList-method unlist,DuckDBGRangesList-method updateObject,DuckDBGRangesList-method width,DuckDBGRangesList-method
Utilities for DuckDBGRangesList objectsDuckDBGRangesList-utils range,DuckDBGRangesList-method