This website contains a collection of publicly available datasets used by the Hemberg Group at the Sanger Institute.
We use SingleCellExperiment Bioconductor S4 class to store our data and scater for quality control and plotting purposes. For each dataset you can find both a
SingleCellExperiment object and a
We welcome contributions to our collection. Please create a pull request to our GitHub repository providing the following information:
bashscript with downloading and processing instructions named as the dataset first author's surname.
Rscript file with the instruction on how to create a
SingleCellExperimentobject named as the dataset first author's surname.
The cell type information must be located in the
cell_type1 column of the
colData slot of the
SingleCellExperiment object. If there are more than one cell type hierarchies please use
- Metadata information about the dataset: publication reference, accession, protocol and size of the dataset. These should be added in
markdownformat to the existing files in the
websitefolder or by creating a new
Some of the dataset hosted here are used as references for scmap, our web-based application for fast unsupervised projection of single cell RNA-seq data.
Please send you feedback/comments/suggestions to Vladimir Kiselev.