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.