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Single-cell RNA-seq datasets for Bioconductor\n\n|Environment|Status|\n|---|---|\n|[BioC-release](https://bioconductor.org/packages/release/data/experiment/html/scRNAseq.html)|[![Release OK](https://bioconductor.org/shields/build/release/data-experiment/scRNAseq.svg)](http://bioconductor.org/checkResults/release/data-experiment-LATEST/scRNAseq/)|\n|[BioC-devel](https://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html)|[![Devel OK](https://bioconductor.org/shields/build/devel/data-experiment/scRNAseq.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/scRNAseq/)|\n\nThis package provides single-cell (mostly RNA-seq) datasets for convenient use by other Bioconductor packages and workflows.\nEach dataset is loaded as a [`SingleCellExperiment`](https://bioconductor.org/packages/SingleCellExperiment) that is immediately ready for further analysis.\nTo get started, install the package and its dependencies from Bioconductor:\n\n```r\n# install.packages(\"BiocManager\")\nBiocManager::install(\"scRNAseq\")\n```\n\nFind datasets of interest:\n\n```r\nsurveyDatasets()\nsearchDatasets(\"brain\")\n```\n\nFetch a dataset as a `SingleCellExperiment`:\n\n```r\nfetchDataset(\"zeisel-brain-2015\", version=\"2023-12-14\")\nfetchDataset(\"baron-pancreas-2016\", \"2023-12-14\", path=\"human\")\n```\n\nAnd add your own datasets to enable re-use by the wider Bioconductor community.\n\nCheck out the [user's guide](https://bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.html) for more details.\n\n## Maintainer notes\n\nIf someone wants to contribute a new dataset, they should follow the instructions in the user's guide.\nThis requires a bit of effort on our (i.e., the package maintainers') part to process a new submission.\n\nOnce a prospective uploader has prepared their `SingleCellExperiment` and its associated metadata,\nthey can be given temporary upload permissions for, e.g., a week, by calling:\n\n```r\ngypsum::setPermissions(\"scRNAseq\", uploaders=list(\n    list(\n        id=\"GITHUB_LOGIN\", \n        asset=\"NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD\",\n        version=\"VERSION_THEY_WANT_TO_UPLOAD\",\n        until=Sys.time() + 7 * 24 * 3600\n    )\n)\n```\n\nOnce the upload is complete, we pull down the dataset for review.\n\n```r\ncache \u003c- tempfile()\ndest \u003c- gypsum::saveVersion(\n    \"scRNAseq\", \n    asset=\"NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD\",\n    version=\"VERSION_THEY_WANT_TO_UPLOAD\",\n    cache=cache\n)\n\n# Check that the saved object is valid. You might need to do this for each\n# subdirectory if they saved multiple objects in a single dataset.\nalabaster.base::validateObject(dest)\n\n# You can also just try loading it for inspection in the R session.\nalabaster.base::readObject(dest)\n\n# Check that the metadata is valid.\nlines \u003c- readLines(file.path(dest, \"_bioconductor.json\"))\ngypsum::validateMetadata(paste(lines, collapse=\"\\n\"))\n```\n\nIf everything looks okay, we can approve the probational dataset.\nOtherwise we reject it.\n\n```r\n# Okay.\ngypsum::approveProbation(\n    \"scRNAseq\", \n    asset=\"NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD\",\n    version=\"VERSION_THEY_WANT_TO_UPLOAD\"\n)\n\n# Not okay.\ngypsum::rejectProbation(\n    \"scRNAseq\", \n    asset=\"NAME_OF_THE_DATASET_THEY_WANT_TO_UPLOAD\",\n    version=\"VERSION_THEY_WANT_TO_UPLOAD\"\n)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fscrnaseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fltla%2Fscrnaseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fscrnaseq/lists"}