Installation | Introduction | Supported Formats | Quick Start | BiocIO Pattern | Lazy Evaluation | Multiple Tables | Connection Management | Next Steps
Package: dbSequence 0.99.1
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:
dbSequence_0.99.1.tar.gz
dbSequence_0.99.1.zip(r-4.7)dbSequence_0.99.1.zip(r-4.6)dbSequence_0.99.1.zip(r-4.5)
dbSequence_0.99.1.tgz(r-4.6-any)dbSequence_0.99.1.tgz(r-4.5-any)
dbSequence_0.99.1.tar.gz(r-4.7-any)dbSequence_0.99.1.tar.gz(r-4.6-any)
dbSequence_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dbSequence/json (API)
| # Install 'dbSequence' in R: |
| install.packages('dbSequence', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dbverse-org/dbsequence/issues
On BioConductor:dbSequence-0.99.1(bioc 3.24)
softwareinfrastructuredataimportsequencingcoveragedatarepresentation
Last updated from:72038b1ab5. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 258 | ||
| linux-devel-x86_64 | OK | 448 | ||
| source / vignettes | OK | 368 | ||
| linux-release-x86_64 | OK | 466 | ||
| macos-release-arm64 | OK | 341 | ||
| macos-oldrel-arm64 | OK | 269 | ||
| windows-devel | OK | 353 | ||
| windows-release | OK | 352 | ||
| windows-oldrel | OK | 336 | ||
| wasm-release | OK | 183 |
Exports:as_grangesasRangescompute_coveragecompute.dbSequencedbSequenceDuckDBFilefileSourcefileSource<-filter_by_overlapspoolread_bamread_bedread_gffread_gff3read_vcftableName
Dependencies:abindAnnotationDbiarrowaskpassassertthatBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolsconnectionscpp11crayoncurlDBIdbplyrdbProjectDelayedArraydigestdplyrduckdbfastmapformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpinspkgconfigpngpurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsrscontractRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8uuidVariantAnnotationvctrswhiskerwithrXMLXVectoryaml
Data Ingestion
Last update: 2026-06-30
Started: 2026-01-15
plyranges API
Introduction | Core Functions | filter_by_overlaps | Multiple Regions | dbSequence to dbSequence | compute_coverage | as_granges | Workflow Example | File Type Restrictions | Next Steps
Last update: 2026-06-30
Started: 2026-01-15
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert objects to GRanges | as_granges as_granges.dbSequence as_granges.default |
| Extract range columns as a view | asRanges,dbSequence-method as_ranges-dbSequence-method |
| Extract genomic ranges from dbSequence objects | asRanges |
| Coercion methods between dbSequence and GRanges | coerce,dbSequence,GRanges-method coerce,GRanges,dbSequence-method coerce-methods |
| Compute coverage over a region | compute_coverage compute_coverage.dbSequence |
| Materialize a dbSequence in DuckDB | compute.dbSequence |
| Constructor for dbSequence objects | dbSequence |
| dbSequence objects | dbSequence-class |
| Constructor for DuckDBFile objects | DuckDBFile |
| DuckDBFile objects | DuckDBFile-class |
| Accessor for file_source slot | fileSource fileSource,dbSequence-method fileSource<- fileSource<-,dbSequence-method |
| Filter ranges by overlap | filter_by_overlaps filter_by_overlaps.dbSequence |
| Import BAM files into DuckDB | import,BamFile,missing,ANY-method |
| Import BED files into DuckDB | import,BEDFile,missing,ANY-method |
| Import character file paths into DuckDB (auto-detect format) | import,character,missing,ANY-method |
| Import FASTA files into DuckDB | import,FastaFile,missing,ANY-method |
| Import GFF files into DuckDB | import,GFFFile,missing,ANY-method |
| Import GTF files into DuckDB | import,GTFFile,missing,ANY-method |
| Import VCF files into DuckDB | import,VcfFile,missing,ANY-method |
| Pool (aggregate) values by grouping columns | pool pool.dbSequence pool.default pool.tbl_dbi pool.tbl_duckdb_connection |
| Read a BAM file into DuckDB | read_bam |
| Read a BED file into DuckDB | read_bed |
| Read a GFF/GTF file into DuckDB | read_gff read_gff3 |
| Read a VCF file into DuckDB | read_vcf |
| Show method for dbSequence objects | show,dbSequence-method |
| Show method for DuckDBFile objects | show,DuckDBFile-method |
| Get table name from dbSequence | tableName tableName,dbSequence-method |
