Package 'bedrockbio'

Title: 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.
Authors: Liam Abbott [aut, cre, cph]
Maintainer: Liam Abbott <[email protected]>
License: GPL (>= 3)
Version: 1.3.0
Built: 2026-04-26 17:40:23 UTC
Source: https://github.com/bedrock-bio/bedrock-bio-client

Help Index

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, and columns.

Examples

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

## 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")
...

Required partition filters (e.g., ancestry = "EUR", protein_id = "A0FGR8")

Value

A lazy tbl backed by DuckDB, compatible with dplyr verbs.

Examples

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

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

## End(Not run)