ParseCELLxGENE: Download CELLxGENE Datasets.

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Download CELLxGENE Datasets.

Description

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

## Not run: 
# 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, need to provide the output folder
ParseCELLxGENE(meta = human.10x.cellxgene.meta, out.folder = "/path/to/output")

## End(Not run)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.