Download CELLxGENE Datasets.

Usage

ParseCELLxGENE(
  meta,
  file.ext = c("rds", "h5ad"),
  out.folder = NULL,
  timeout = 3600,
  quiet = FALSE,
  parallel = TRUE
)

Arguments

meta: Metadata used to download, can be from ExtractCELLxGENEMeta, should contain dataset_id, rds_id/h5ad_id (depend on file.ext) and name columns.
file.ext: The valid file extension for download. When NULL, use "rds" and "h5ad". Default: c("rds", "h5ad").
out.folder: The output folder. Default: NULL (current working directory).
timeout: Maximum request time. Default: 3600.
quiet: Logical value, whether to show downloading progress. Default: FALSE (show).
parallel: Logical value, whether to download parallelly. Default: TRUE. When "libcurl" is available for download.file, the parallel is done by default (parallel can be FALSE).

Value

Dataframe contains failed datasets or NULL.

References

https://gist.github.com/ivirshup/f1a1603db69de3888eacb4bdb6a9317a

Examples

# # all available datasets
# all.cellxgene.datasets = ShowCELLxGENEDatasets()
# # human 10x v2 and v3 datasets
# human.10x.cellxgene.meta = ExtractCELLxGENEMeta(all.samples.df = all.cellxgene.datasets, assay = c("10x 3' v2", "10x 3' v3"),
#                                                 organism = "Homo sapiens")
# # download
# ParseCELLxGENE(meta = human.10x.cellxgene.meta, out.folder = "/path/to/output")