Data

1. PBMC3K dataset, Seurat and AnnData

2,700 peripheral blood mononuclear cells (PBMC) from 10X genomics

Satija Lab (2019). pbmc3k.SeuratData: 2,700 peripheral blood mononuclear cells (PBMC) from 10X genomics. R package version 3.0.0.

2. CITE-seq bone marrow, Seurat and AnnData

The CITE-seq data from human bone marrow cells were measured cellular transcriptomes alongside 25 cell-surface proteins representing well-characterized markers. In the Seurat object, the protein count matrix is in the ADT assay. In the AnnData object, the protein count matrix is concatenate with RNA count matrix and the prefix of protein is adt.

Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck III, W. M., ... & Satija, R. (2019). Comprehensive Integration of Single-Cell Data. Cell.

3. Endoderm Full,Seurat and AnnData

The mouse endoderm development data is from E8.75 gut tube. The data can also be explored at https://endoderm-explorer.com

Nowotschin, S., Setty, M., Kuo, Y. Y., Liu, V., Garg, V., Sharma, R., ... & Church, D. M. (2019). The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature, 569(7756), 361.

4. Endoderm Downsampled, Seurat and AnnData

The UMI count of each cell is downsampled by a uniform distribution from 5% to 100%.