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_v2.3.1.parquet to /tmp/RtmpHNRMD2/sample_hca2024_v2.3.1.parquet
#> duckdb is keeping downloaded extensions in a temporary directory:
#> ℹ /tmp/RtmpHNRMD2/duckdb/extensions
#> This is removed when the R session ends, so extensions are re-downloaded each session.
#> ℹ To keep them, point `options(duckdb.extension_directory =)` or the `DUCKDB_EXTENSION_DIRECTORY` environment variable at a permanent path.
#> # A query:  ?? x 36
#> # Database: DuckDB 1.5.4 [unknown@Linux 6.17.0-1020-azure:R 4.6.1/:memory:]
#>    cell_id dataset_id           sample_id sample_ experiment___ run_from_cell_id
#>      <dbl> <chr>                <chr>     <chr>   <chr>         <chr>           
#>  1      15 842c6f5d-4a94-4eef-… 1119f482… 1119f4… ""            NA              
#>  2      16 842c6f5d-4a94-4eef-… 1119f482… 1119f4… ""            NA              
#>  3      17 842c6f5d-4a94-4eef-… 1119f482… 1119f4… ""            NA              
#>  4      18 842c6f5d-4a94-4eef-… 1119f482… 1119f4… ""            NA              
#>  5      19 842c6f5d-4a94-4eef-… 1119f482… 1119f4… ""            NA              
#>  6      20 842c6f5d-4a94-4eef-… 1119f482… 1119f4… ""            NA              
#>  7      14 842c6f5d-4a94-4eef-… 1119f482… 1119f4… ""            NA              
#>  8       2 842c6f5d-4a94-4eef-… 1f755b9b… 1f755b… ""            NA              
#>  9       3 842c6f5d-4a94-4eef-… 1f755b9b… 1f755b… ""            NA              
#> 10       4 842c6f5d-4a94-4eef-… 1f755b9b… 1f755b… ""            NA              
#> # ℹ more rows
#> # ℹ 30 more variables: sample_heuristic <chr>, age_days <int>,
#> #   tissue_groups <chr>, nFeature_expressed_in_sample <int>, 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>, scDblFinder.class <chr>,
#> #   sample_chunk <int>, cell_chunk <int>, sample_pseudobulk_chunk <int>, …