Package: DuckDBGRanges 0.99.1

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, 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_0.99.1.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://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

Conda:

dataimportdatarepresentationinfrastructuresequencingsoftware

4.69 score 1 packages 65 exports 43 dependencies

Last updated from:d4feb32232. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING235
linux-devel-x86_64NOTE437
source / vignettesOK317
linux-release-x86_64NOTE493
macos-release-arm64NOTE393
macos-oldrel-arm64NOTE310
windows-devel-x86_64NOTE921
windows-release-x86_64NOTE861
windows-oldrel-x86_64NOTE945
wasm-releaseOK179

Exports:.has_row_number.keycolsas.data.framecountOverlapsdbconndimtblsdimtbls<-disjoindistancedistanceToNearestDuckDBGRangesDuckDBGRangesListduplicatedelementMetadataelementMetadata<-elementNROWSendextractROWSfindOverlapsflankfollowgapsgenome<-getListElementheadintersectis.unsortedmatchnarrownearestorderoverlapsAnypgappintersectprecedepromoterspsetdiffpunionrangesrankrealizereduceresizerestrictseqinfoseqlengths<-seqnamessetdiffshiftshowslidingWindowssortsplitstartstrandsubsetByOverlapstailtblconnterminatorstiletrimunionuniqueupdateObjectwidth

Dependencies:abindarrowassertthatBiocGenericsbitbit64blobclicpp11DBIdbplyrDelayedArraydplyrduckdbDuckDBDataFramegenericsGenomicRangesglueIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpurrrR6rlangS4ArraysS4VectorsSeqinfoSparseArraystringistringrtibbletidyrtidyselectutf8vctrswithrXVector

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: 2026-07-06
Started: 2026-07-06

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

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

Readme and manuals

Help Manual

Help pageTopics
DuckDBGRanges objects.has_row_number,DuckDBGRanges-method .keycols,DuckDBGRanges-method as.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 head,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 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 objects.has_row_number,DuckDBGRangesList-method .keycols,DuckDBGRangesList-method coerce,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 head,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