All datasets hosted in this website are analysed using the Seurat package developed by the Satija Lab in NYGC.

For more information click here

1. Project Summary

The Project Summary tab gives a short description about the selected dataset and basic information such as organism, total number of cells, number of cells in each cluster, total number of genes and number of dimensions used in the analysis

2. tSNE Plots

The Compare tSNE plots displays two plots with same options. Users can choose the Dimensionality reduction method as well as pick between categories, clusters and gene expression. There are additional options to change colors of gene expression plot (also called feature plot) as well as subselect cells based on clusters or a range of numeric values

The Interactive tSNE/uMAP Plot displays the same as in the Compare tSNE plots tab except these plots are interactive. Users can zoom in, subselect and hover over for point information

3. Biplot

The Biplot is similar to seurat's plot with the 'overlap' option. Users specify dimensionality reduction method, 2 genes and the expression limit of each gene in terms of logUMI to view a bigene plot based on the expression of the two genes. The tab also shows a table with the number of cells in each Cell group expression the 2 genes

4. Differential Expression

The differential expression tab generates a table of marker genes specific to a cell group as well as plots showing the expression of each of those marker genes in each cell group.By default, the results displayed are each cell group again every other cell group. User can, however, find marker genes by checking the Check to choose a different category to compare option and selecting one cell group that can be compared against one or multiple other groups

5. Seurat heatmap

The Seurat heatmap tap generates an expression heatmap for given cells and marker genes from the table in Differential Expression tab

6. Gene Expression plots

The Gene Expression plots displays the same 3 expression, violin and ridge plots as in the Differential Expression tab. However, instead of having to select from a table, in this tab, users can manually specify the gene name they are interested in

The Cluster-wise Gene Expression tab shows a general dimension reduction plot as well as a gene expression plot along with a table of list of genes present in the data ordered by the percent of cells they are present in and their average expression across these cells

The Gene-Cellgroup Dotplot tab displays a dotplot like the one here where the genes are rows, cell-groups are the columns and the size of the dots show percentage of cells expressing that gene. Users please upload text files with one gene per line

7. Ligand receptor Pairs

The Ligand Receptor Pairs tab generates a table of all possible ligand receptor pairs (from FANTOM5 ) between each of the cell groups. Expression of each receptor/ligand gene per cell group is counted if it is expressed in at least 20% of the cells (by default. Users can change this and go upto 100%). This tab also displays a bigene plot for each of the ligand-receptor pair in the table

The Ligand Receptor Network tab displays a network where each cell group is a node and the edges denote the frequency of ligand-receptor pairs between the nodes. This tab also performs GO analysis on the selected pairs and displays the results in a table

For unknown errors or support, email bapoorva@pennmedicine.upenn.edu