This browser allows the exploration of single cell data for simultaneously profiled RNA expression and chromatin accessibility per cell.
The data is split into 4 main groups.
"Gene Expression" contains normalized gene expression, and "Gene Expression (integrated)" contains the Seurat batch integrated normalized expression results.
"Chromatin accessibility" contains the normalized ATACseq accessibility scores per peak.
"TF Motif Accessibility" contains the chromVar based transcription factor activities.
With the Shiny app, users can interactively explore their single-cell data, varying the cell information / gene expression to plot. Furthermore, these plots can be exported into PDF / PNG for presentations / publications. Users can also click on the "Toggle graphics controls" or "Toggle plot controls" to fine-tune certain aspects of the plots e.g. point size.
Within each dataset there seven tabs, with the opening page showing the first tab "CellInfo vs GeneExpr", plotting both cell information and gene expression side-by-side on reduced dimensions e.g. UMAP. Users can click on the toggle on the bottom left corner to display the cell numbers in each cluster / group and the number of cells expressing a gene. The next two tabs are similar, showing either two cell information side-by-side (second tab: "CellInfo vs CellInfo") or two gene expressions side-by-side (third tab: "GeneExpr vs GeneExpr").
The fourth tab "Gene coexpression" blends the gene expression of two genes, given by two different colour hues, onto the same reduced dimensions plot. Furthermore, the number of cells expressing either or both genes are given.
The fifth tab "Violinplot / Boxplot" plots the distribution of continuous cell information e.g. nUMI or module scores or gene expression across each cluster / group using violin plots or box plots.
The sixth tab "Proportion plot" plots the composition of different clusters / groups of cells using proportion plots. Users can also plot the cell numbers instead of proportions.
The seventh tab "Bubbleplot / Heatmap" allows users to visualise the expression of multiple genes across each cluster / group using bubbleplots / heatmap. The genes (rows) and groups (columns) can be furthered clustered using hierarchical clustering.
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.
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.
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.
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.
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.
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.
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.
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.
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.
The Space Omics and Medical Atlas (SOMA) and international astronaut biobank
Overbey, E. G., Kim, J.K., Tierney, B. T. et al.
Nature (2024)
doi: 10.1038/s41586-024-07639-y
Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight
Kim, J.K., Tierney B. T., Overbey, E. G. et al.
Nature Commun. (2024)
doi: 10.1038/s41467-024-49211-2