| Title: | Open-Access Computational Biology Datasets |
| Version: | 1.3.0 |
| 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-client |
| BugReports: | https://github.com/bedrock-bio/bedrock-bio-client/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: | 2026-04-26 17:14:02 UTC; runner |
| Author: | Liam Abbott [aut, cre, cph] |
| Maintainer: | Liam Abbott <liam@bedrock.bio> |
| Repository: | CRAN |
| Date/Publication: | 2026-04-28 20:00:03 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:
Report bugs at https://github.com/bedrock-bio/bedrock-bio-client/issues
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)