Classical hierarchy of haematopoietic cells

Trajectory analysis of 21 cell clusters

Immunophenotype of each population




Cell Prediction

Original Atlas




The interface is to help search the gene expression of any given gene in single cells grouped by 21 transcriptional clusters or 28 immunophenotypic cell types, and displayed via boxplot.


1. Enter a gene symbol in the search box to instantly visualize the expression data (Runx1 is displayed by default).

2. Optionally, click the button below the search box to switch the display of cells grouped in two forms (RNA cluster is displayed by default).


The interface is designed to predict the blood cell types for single-cell RNA-seq datasets. Scmap is used to achieve cell type prediction and generate the visualization plot.


1. Upload a tab-delimited format file containing the expression matrix. Each row should be a gene symbol and each column should be a single cell (UMI is recommended).

2. Click the Run button to start prediction. Cell Prediction (left panel) displays the single cells (highlighted in red color) in the ABC reference with minimum distances to the cells in the query. Original Atlas (right panel) displays the distributions of RNA clusters in the ABC reference. The table below summarizes the predicted cell type and prediction score for each single cell.

3. The size of file is less than 50M, which is about 1000 cells.

Citation: Dong, F., Hao, S., Zhang, S. et al. Differentiation of transplanted haematopoietic stem cells tracked by single-cell transcriptomic analysis. Nat Cell Biol 22, 630–639 (2020).

This work is supported by Atlas of Blood Cells (ABC)