https://github.com/ltla/scrnaseq
Clone of the Bioconductor repository for the scRNAseq package.
https://github.com/ltla/scrnaseq
bioconductor
Last synced: about 1 year ago
JSON representation
Clone of the Bioconductor repository for the scRNAseq package.
- Host: GitHub
- URL: https://github.com/ltla/scrnaseq
- Owner: LTLA
- Created: 2019-06-09T22:05:30.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2025-01-18T22:52:42.000Z (over 1 year ago)
- Last Synced: 2025-03-24T06:05:03.121Z (about 1 year ago)
- Topics: bioconductor
- Language: R
- Homepage: http://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html
- Size: 50.1 MB
- Stars: 25
- Watchers: 4
- Forks: 12
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Single-cell RNA-seq datasets for Bioconductor
|Environment|Status|
|---|---|
|[BioC-release](https://bioconductor.org/packages/release/data/experiment/html/scRNAseq.html)|[](http://bioconductor.org/checkResults/release/data-experiment-LATEST/scRNAseq/)|
|[BioC-devel](https://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html)|[](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/scRNAseq/)|
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`](https://bioconductor.org/packages/SingleCellExperiment) that is immediately ready for further analysis.
To get started, install the package and its dependencies from Bioconductor:
```r
# install.packages("BiocManager")
BiocManager::install("scRNAseq")
```
Find datasets of interest:
```r
surveyDatasets()
searchDatasets("brain")
```
Fetch a dataset as a `SingleCellExperiment`:
```r
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](https://bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.html) 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:
```r
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.
```r
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.
```r
# 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"
)
```