| Title: | Open-Access Computational Biology Datasets |
| Version: | 2.0.0 |
| 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 (≥ 4.2) |
| Imports: | curl, DBI, dbplyr, dplyr, duckdb, jsonlite |
| Suggests: | testthat (≥ 3.0.0), withr |
| Config/testthat/edition: | 3 |
| OS_type: | unix |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.3 |
| NeedsCompilation: | no |
| Packaged: | 2026-07-02 13:03:40 UTC; runner |
| Author: | Liam Abbott [aut, cre, cph] |
| Maintainer: | Liam Abbott <liam@bedrock.bio> |
| Repository: | CRAN |
| Date/Publication: | 2026-07-02 13:20:07 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 namespace: its name, citation, license, context, and tables
Description
Describe a namespace: its name, citation, license, context, and tables
Usage
describe_namespace(name)
Arguments
name |
Namespace identifier. |
Value
A named list with name, citation, license, context, and
tables (fully-qualified table identifiers). Use describe_table() for
per-table details.
Examples
## Not run:
library(bedrockbio)
describe_namespace("ukb_ppp")$tables
## End(Not run)
Describe a table: its context, columns, and partitions
Description
Describe a table: its context, columns, and partitions
Usage
describe_table(name)
Arguments
name |
Table identifier. |
Value
A named list with name, context, columns (each with name,
type, description, nullable), and partitions (a named list of
partition column to values and default). Filter on partition columns
for fastest reads.
Examples
## Not run:
library(bedrockbio)
describe_table("ukb_ppp.pqtls")$name
## End(Not run)
List available namespaces (data sources)
Description
List available namespaces (data sources)
Usage
list_namespaces()
Value
A character vector of namespace identifiers.
Examples
## Not run:
library(bedrockbio)
list_namespaces()
## End(Not run)
List available tables, optionally filtered to one namespace
Description
List available tables, optionally filtered to one namespace
Usage
list_tables(namespace = NULL)
Arguments
namespace |
If given, return only that namespace's tables; otherwise all tables. |
Value
A character vector of fully-qualified table identifiers.
Examples
## Not run:
library(bedrockbio)
list_tables("ukb_ppp")
## End(Not run)
Lazily query a table
Description
Lazily query a table
Usage
load_table(name)
Arguments
name |
Table identifier. |
Value
A lazy tbl backed by DuckDB, compatible with dplyr verbs. Filter
on partition columns (see describe_table()) for fastest reads.
Examples
## Not run:
library(bedrockbio)
library(dplyr)
load_table("dbsnp.vcf") |>
filter(assembly == "GRCh38", chromosome == "22") |>
select(rsid, position, ref_allele, alt_allele) |>
head(5) |>
collect()
## End(Not run)