Package: dbSequence 0.99.0

Edward C. Ruiz

dbSequence: DuckDB-Backed Interface for Large-Scale Genomic Data

Provides a DuckDB-backed infrastructure for working with large-scale genomic data that exceeds available memory. Supports lazy evaluation of genomic ranges and efficient overlap queries. Integrates with Bioconductor classes (GRanges, BiocIO) and provides plyranges-compatible API.

Authors:Edward C. Ruiz [aut, cre]

dbSequence_0.99.0.tar.gz
dbSequence_0.99.0.zip(r-4.7)dbSequence_0.99.0.zip(r-4.6)dbSequence_0.99.0.zip(r-4.5)
dbSequence_0.99.0.tgz(r-4.6-any)dbSequence_0.99.0.tgz(r-4.5-any)
dbSequence_0.99.0.tar.gz(r-4.7-any)dbSequence_0.99.0.tar.gz(r-4.6-any)
dbSequence_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dbSequence/json (API)
NEWS

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

Bug tracker:https://github.com/dbverse-org/dbsequence-r/issues

On CRAN:

Conda:

infrastructuredataimportsequencingcoveragedatarepresentation

3.64 score 11 scripts 16 exports 93 dependencies

Last updated from:c877069a83. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE227
linux-devel-x86_64OK411
source / vignettesOK321
linux-release-x86_64OK451
macos-release-arm64OK303
macos-oldrel-arm64OK308
windows-develOK360
windows-releaseOK359
windows-oldrelOK335
wasm-releaseOK174

Exports:as_grangesasRangescompute_coveragecompute.dbSequencedbSequenceDuckDBFilefileSourcefileSource<-filter_by_overlapspoolread_bamread_bedread_gffread_gff3read_vcftableName

Dependencies:abindAnnotationDbiarrowaskpassassertthatBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolsconnectionscpp11crayoncurlDBIdbplyrdbProjectDelayedArraydigestdplyrduckdbfastmapformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpinspkgconfigpngpurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsrscontractRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8uuidVariantAnnotationvctrswhiskerwithrXMLXVectoryaml

Data Ingestion

Rendered fromdata-ingestion.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-04-29
Started: 2026-01-15

plyranges API

Rendered fromplyranges-api.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-04-29
Started: 2026-01-15

Readme and manuals

Help Manual

Help pageTopics
Convert objects to GRangesas_granges as_granges.dbSequence as_granges.default
Extract range columns as a viewasRanges,dbSequence-method as_ranges-dbSequence-method
Extract genomic ranges from dbSequence objectsasRanges
Coercion methods between dbSequence and GRangescoerce,dbSequence,GRanges-method coerce,GRanges,dbSequence-method coerce-methods
Compute coverage over a regioncompute_coverage compute_coverage.dbSequence
Materialize a dbSequence in DuckDBcompute.dbSequence
Constructor for dbSequence objectsdbSequence
dbSequence objectsdbSequence-class
Constructor for DuckDBFile objectsDuckDBFile
DuckDBFile objectsDuckDBFile-class
Accessor for file_source slotfileSource fileSource,dbSequence-method fileSource<-,dbSequence-method
Replacement method for file_source - BLOCKEDfileSource<-
Filter ranges by overlapfilter_by_overlaps filter_by_overlaps.dbSequence
Import BAM files into DuckDBimport,BamFile,missing,ANY-method
Import BED files into DuckDBimport,BEDFile,missing,ANY-method
Import character file paths into DuckDB (auto-detect format)import,character,missing,ANY-method
Import FASTA files into DuckDBimport,FastaFile,missing,ANY-method
Import GFF files into DuckDBimport,GFFFile,missing,ANY-method
Import GTF files into DuckDBimport,GTFFile,missing,ANY-method
Import VCF files into DuckDBimport,VcfFile,missing,ANY-method
Pool (aggregate) values by grouping columnspool pool.dbSequence pool.default pool.tbl_dbi pool.tbl_duckdb_connection
Read a BAM file into DuckDBread_bam
Read a BED file into DuckDBread_bed
Read a GFF/GTF file into DuckDBread_gff read_gff3
Read a VCF file into DuckDBread_vcf
Show method for dbSequence objectsshow,dbSequence-method
Show method for DuckDBFile objectsshow,DuckDBFile-method
Get table name from dbSequencetableName tableName,dbSequence-method