Package {bedrockbio}

Title: Open-Access Computational Biology Datasets
Version: 1.4.0
Description: Efficiently access the 'Bedrock Bio' library of open-access computational biology datasets. Lazily query datasets backed by 'DuckDB' and 'Apache Iceberg', with support for predicate pushdown and column projection to the cloud storage backend. This enables quick, iterative access to otherwise massive, unwieldy datasets without downloading them in full. See https://bedrock.bio for available datasets and documentation.
Language: en-US
License: GPL (≥ 3)
URL: https://bedrock.bio, https://github.com/bedrock-bio/bedrock-bio
BugReports: https://github.com/bedrock-bio/bedrock-bio/issues
Depends: R (≥ 4.1)
Imports: curl, DBI, dbplyr, dplyr, duckdb, jsonlite
Suggests: testthat (≥ 3.0.0)
Config/testthat/edition: 3
OS_type: unix
Encoding: UTF-8
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-05-24 02:09:10 UTC; runner
Author: Liam Abbott [aut, cre, cph]
Maintainer: Liam Abbott <liam@bedrock.bio>
Repository: CRAN
Date/Publication: 2026-05-28 13:50:08 UTC

bedrockbio: Open-Access Computational Biology Datasets

Description

Efficiently access the 'Bedrock Bio' library of open-access computational biology datasets. Lazily query datasets backed by 'DuckDB' and 'Apache Iceberg', with support for predicate pushdown and column projection to the cloud storage backend. This enables quick, iterative access to otherwise massive, unwieldy datasets without downloading them in full. See https://bedrock.bio for available datasets and documentation.

Author(s)

Maintainer: Liam Abbott liam@bedrock.bio [copyright holder]

See Also

Useful links:

Describe a namespace's metadata, citation, license, and tables

Description

Describe a namespace's metadata, citation, license, and tables

Usage

describe_namespace(name)

Arguments

name

Namespace identifier (e.g., "ukb_ppp")

Value

A named list with id, name, description, source_url, license, instructions, citation, and tables (character vector of fully-qualified table identifiers). Use describe_table() for per-table details.

Examples

## Not run: 
library(bedrockbio)
info <- describe_namespace("ukb_ppp")
info$tables

## End(Not run)

Describe a table's metadata, citation, and columns

Description

Describe a table's metadata, citation, and columns

Usage

describe_table(name)

Arguments

name

Table identifier (e.g., "ukb_ppp.pqtls")

Value

A named list with name, description, citation, source_url, license, partition_by, sort_by, and columns.

Examples

## Not run: 
library(bedrockbio)
info <- describe_table("ukb_ppp.pqtls")
info$name

## End(Not run)

List available namespaces (data sources) in the Bedrock Bio library

Description

List available namespaces (data sources) in the Bedrock Bio library

Usage

list_namespaces()

Value

A character vector of namespace identifiers

Examples

## Not run: 
library(bedrockbio)
list_namespaces()

## End(Not run)

List available tables in the Bedrock Bio library

Description

List available tables in the Bedrock Bio library

Usage

list_tables()

Value

A character vector of table identifiers

Examples

## Not run: 
library(bedrockbio)
list_tables()

## End(Not run)

Lazily query a table

Description

Lazily query a table

Usage

load_table(name)

Arguments

name

Table identifier (e.g., "ukb_ppp.pqtls")

Value

A lazy tbl backed by DuckDB, compatible with dplyr verbs. Use describe_table() to see partition columns and per-column allowed values; filter on partition columns for fastest reads.

Examples

## Not run: 
library(bedrockbio)
library(dplyr)

df <- load_table("dbsnp.vcf") |>
  filter(assembly == "GRCh38", chromosome == "22") |>
  select(rsid, position, ref_allele, alt_allele) |>
  head(5) |>
  collect()

## End(Not run)