Single-cell RNA-seq datasets for Bioconductor

Environment	Status
BioC-release
BioC-devel

This package provides single-cell (mostly RNA-seq) datasets for convenient use by other Bioconductor packages and workflows. Each dataset is loaded as a SingleCellExperiment that is immediately ready for further analysis. To get started, install the package and its dependencies from Bioconductor:

# install.packages("BiocManager")
BiocManager::install("scRNAseq")

Find datasets of interest:

surveyDatasets()
searchDatasets("brain")

Fetch a dataset as a SingleCellExperiment:

fetchDataset("zeisel-brain-2015", version="2023-12-14")
fetchDataset("baron-pancreas-2016", "2023-12-14", path="human")

And add your own datasets to enable re-use by the wider Bioconductor community.

Check out the user’s guide for more details.

Maintainer notes

If someone wants to contribute a new dataset, they should follow the instructions in the user’s guide. This requires a bit of effort on our (i.e., the package maintainers’) part to process a new submission.

Once a prospective uploader has prepared their SingleCellExperiment and its associated metadata, they can be given temporary upload permissions for, e.g., a week, by calling:

gypsum::setPermissions("scRNAseq", uploaders=list(
    list(
        id="GITHUB_LOGIN", 
        asset="NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD",
        version="VERSION_THEY_WANT_TO_UPLOAD",
        until=Sys.time() + 7 * 24 * 3600
    )
)

Once the upload is complete, we pull down the dataset for review.

cache <- tempfile()
dest <- gypsum::saveVersion(
    "scRNAseq", 
    asset="NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD",
    version="VERSION_THEY_WANT_TO_UPLOAD",
    cache=cache
)

# Check that the saved object is valid. You might need to do this for each
# subdirectory if they saved multiple objects in a single dataset.
alabaster.base::validateObject(dest)

# You can also just try loading it for inspection in the R session.
alabaster.base::readObject(dest)

# Check that the metadata is valid.
lines <- readLines(file.path(dest, "_bioconductor.json"))
gypsum::validateMetadata(paste(lines, collapse="\n"))

If everything looks okay, we can approve the probational dataset. Otherwise we reject it.

# Okay.
gypsum::approveProbation(
    "scRNAseq", 
    asset="NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD",
    version="VERSION_THEY_WANT_TO_UPLOAD"
)

# Not okay.
gypsum::rejectProbation(
    "scRNAseq", 
    asset="NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD",
    version="VERSION_THEY_WANT_TO_UPLOAD"
)