URL pointing to the sample metadata file, which is smaller and for test, demonstration, and vignette purposes only

Usage

SAMPLE_DATABASE_URL

Format

An object of class character of length 1.

Source

Shen et al.,2026

Value

Character scalar consisting of the URL/URLs

References

Shen, M., Y. Gao, N. Liu, D. Bhuva, M. Milton, J. Henao, J. Andrews, E. Yang, C. Zhan, N. Liu, S. Si, J. W. Hutchison, M. H. Shakeel, M. Morgan, A. T. Papenfuss, J. Iskander, J. M. Polo, and S. Mangiola. "cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data." bioRxiv (2026). doi:10.64898/2026.04.14.718336.

Examples

get_metadata(cloud_metadata = SAMPLE_DATABASE_URL, cache_directory = tempdir())
#> ℹ Downloading 1 file, totalling 0 GB
#> ℹ Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-metadata/sample_hca2024_v2.4.0.parquet to /tmp/RtmpxBq4x1/sample_hca2024_v2.4.0.parquet
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpxBq4x1/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> # A query:  ?? x 31
#> # Database: DuckDB 1.5.6 [unknown@Linux 6.17.0-1022-azure:R 4.6.1/:memory:]
#>    cell_id dataset_id    sample_id feature_count age_days nFeature_expressed_i…¹
#>      <dbl> <chr>         <chr>             <int>    <int>                  <int>
#>  1      14 842c6f5d-4a9… 1119f482…         33145    14600                   1547
#>  2      15 842c6f5d-4a9… 1119f482…         33145    14600                   1701
#>  3      16 842c6f5d-4a9… 1119f482…         33145    14600                   2438
#>  4      17 842c6f5d-4a9… 1119f482…         33145    14600                   2122
#>  5      18 842c6f5d-4a9… 1119f482…         33145    14600                   1894
#>  6      19 842c6f5d-4a9… 1119f482…         33145    14600                   1876
#>  7      20 842c6f5d-4a9… 1119f482…         33145    14600                   1441
#>  8       2 842c6f5d-4a9… 1f755b9b…         33145    14600                   1342
#>  9       5 842c6f5d-4a9… 1f755b9b…         33145    14600                   1820
#> 10       4 842c6f5d-4a9… 1f755b9b…         33145    14600                   1514
#> # ℹ more rows
#> # ℹ abbreviated name: ¹nFeature_expressed_in_sample
#> # ℹ 25 more variables: nCount_RNA <dbl>, empty_droplet <lgl>,
#> #   cell_type_unified_ensemble <chr>, is_immune <lgl>,
#> #   subsets_Mito_percent <int>, subsets_Ribo_percent <int>,
#> #   high_mitochondrion <lgl>, high_ribosome <lgl>, alive <lgl>,
#> #   scDblFinder.class <chr>, file_id_cellNexus_single_cell <chr>, …