Introduction
To be added
Please cite the PD spatial database as:
Citation will be updated.
Gene Summary
Differential expressed genes in different time points compared to sham
* Wilcoxon Rank Sum test were used to identify differentially expressed genes between two groups of cells
* pct: The percentage of cells where the gene detected in the group
* avg_log2FC: log fold-chage of the average expression between the two groups.
* p_val_adj: Adjusted p-value, based on bonferroni correction using all genes in the dataset
Spatial gene expression: Spatial plot
Spatial geneset score: Spatial plot
Cell information vs gene expression on reduced dimensions
In this tab, users can visualise both cell information and gene expression side-by-side on low-dimensional representions.Dimension Reduction
Cell information vs cell information on dimension reduction
In this tab, users can visualise two cell informations side-by-side on low-dimensional representions.Dimension Reduction
Gene expression vs gene expression on dimension reduction
In this tab, users can visualise two gene expressions side-by-side on low-dimensional representions.Dimension Reduction
Coexpression of two genes on reduced dimensions
In this tab, users can visualise the coexpression of two genes on low-dimensional representions.Dimension Reduction
Cell information / gene expression violin plot / box plot
In this tab, users can visualise the gene expression or continuous cell information (e.g. Number of UMIs / module score) across groups of cells (e.g. libary / clusters).Proportion / cell numbers across different cell information
In this tab, users can visualise the composition of single cells based on one discrete cell information across another discrete cell information. Usage examples include the library or cellcycle composition across clusters.Gene expression bubbleplot / heatmap
In this tab, users can visualise the gene expression patterns of multiple genes grouped by categorical cell information (e.g. library / cluster).The normalised expression are averaged, log-transformed and then plotted.
GeneSet Score violin plot / box plot
In this tab, users can visualise a total of 24604 GeneSet score from MsigDB across groups of cells (e.g. libary / clusters).All rights reserved.
Copyright 2022 Steno Diabetes Center Aarhus (SDCA); Aarhus University
Created by DREAMlab, Department of Biomedicine, Aarhus University
Get in touch with us: lin.lin@biomed.au.dk
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