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dbMatrix - Database-Backed Matrix Classes and Operations

Provides S4 classes and methods for storing dense and sparse matrices in 'DuckDB' databases. The package supports constructing database-backed matrices from base R and 'Matrix' objects, extracting slices and summaries, performing arithmetic and selected linear algebra operations, and materializing results for larger-than-memory workflows. It integrates with 'dbProject' to keep database paths, live connections, and lazy matrix tables synchronized across interactive analyses.

Last updated

cpp

6.18 score 2 stars 14 scripts 452 downloads

dbProject - Database Connection Management and Utilities for 'dbverse'

Provides an R6-based project container for managing 'DuckDB' connections, reconnecting lazy database tables after session restarts, and storing metadata for database-backed objects used by packages in the 'dbverse'. The package supplies S4 base classes and generics for database-backed data, helpers for validating 'DuckDB' connections and table names, utilities for creating persistent database views, and methods for writing and restoring pinned lazy tables through the 'pins' package. These tools help package authors and analysts keep database paths, cached connections, and table references synchronized across interactive sessions and project directories.

Last updated

6.13 score 1 stars 3 dependents 423 downloads

dbSpatial - Spatial Data Operations for Database-Backed Geometries

Provides database-backed spatial geometry classes and methods for working with vector spatial data in 'DuckDB'. The package supports loading, converting, querying, joining, and measuring spatial geometries through familiar 'sf'-style interfaces while keeping geometry columns lazy inside the database. It integrates with 'dbProject' to preserve database paths, live connections, and spatial table metadata across interactive sessions. The package follows the Simple Features framework described by Pebesma (2018) <doi:10.32614/RJ-2018-009> and uses DuckDB's spatial extension <https://duckdb.org/docs/stable/core_extensions/spatial/overview.html>.

Last updated

5.83 score 2 stars 16 scripts 432 downloads

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.

Last updated

softwareinfrastructuredataimportsequencingcoveragedatarepresentation

4.78 score 12 scripts

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.

Last updated

softwareinfrastructuredataimportsequencingcoveragedatarepresentation

4.78 score 12 scripts 685 downloads