ParseHCA: Download Human Cell Atlas Datasets.

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

Download Human Cell Atlas Datasets.

Description

Download Human Cell Atlas Datasets.

Usage

ParseHCA(
  meta,
  file.ext = c("rds", "rdata", "h5", "h5ad", "loom"),
  out.folder = NULL,
  timeout = 3600,
  quiet = FALSE,
  parallel = TRUE
)

Arguments

meta	Metadata used to download, can be from ExtractHCAMeta, should contain entryId and name catalog.
file.ext	The valid file extension for download. When NULL, use "rds", "rdata", "h5", "h5ad", "loom". Default: c("rds", "rdata", "h5", "h5ad", "loom").
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 projects or NULL.

Examples

## Not run: 
# all available projects
all.hca.projects <- ShowHCAProjects()
# all human and 10x 3' v2
all.human.10x.projects <- ExtractHCAMeta(
  all.projects.df = all.hca.projects,
  organism = "Homo sapiens",
  protocol = c("10x 3' v2", "10x 3' v3")
)
# download, need users to provide the output folder
ParseHCA(meta = all.human.10x.projects, out.folder = "/path/to/output")

## End(Not run)

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