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"
)