SingleStudy - Cell Taxonomy - CNCB-NGDC

Study

Journal: ASDF
Year: xxxx
PMID: 123456

Abstract

This panel shows the detailed samples contained in this study.

Sample ID	Species	Tissue	Cell number

Dimensional reduction

This panel visualizes high-dimensional datasets by t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP).

Cluster type

tSNE
tSNE 3D
UMAP
UMAP 3D

This panel shows the number of cell types in this study.

Sample ID	Cell type	Tissue	Number of cells

Silhouette coefficient

This panel measures the goodness of cell clusters and higher Silhouette coefficient indicates larger difference between intra-cluster distance and inter-cluster distance.

Sample ID	Cell type	ID	Silhouette coefficient The Silhouette Coefficient ranges from -1 to 1, and 1 means clusters are well apart from each other, 0 means clusters are indifferent, and -1 means clusters are defined in the wrong way.

Heterogeneity of cell population

A purity score is calculated to assess the heterogeneous state of each cell type, and you can choose the study with higher score to better represent the cell type.

Sample ID	Cell type	ID	ROGUE index ROGUE is calculated to accurately quantify the purity of identified cell clusters. A ROGUE value greater than 0.9 indicates a cell cluster with high purity.

Cell marker evaluation

This panel shows the evaluation of all gene markers in cell types you select, including fold change between this cell type and other cell types, as well as statistical significance.

Sample ID

Cell type

Gene

Sample ID	Cell type	Cell marker	P value	Avg log2FC	Pct.cell type The expression percentage of this gene in this cell type	Pct.others The expression percentage of this gene in other cell types	FDR

Cell type specificity

Jensen–Shannon (JS) divergence score (0-1) is calculated to quantify the cell type specificity of one marker gene (Cabili MN et al., 2011 ). The JS score greater than 0.6 indicates the higher specificity.

Sample ID

Gene name

Select a gene to see the cell types in which this gene is specifically expressed.