This Shiny App allows interactive interface with the data from our single embryo single cell rabbit gastrulation study (https://www.biorxiv.org/content/10.1101/2022.11.13.516304v2).

Here you can find data describing ~115k high quality cells obtained from 108 rabbit embryos from E6.0-E8.6. Since we sequence the cells from each embryo separately, we can provide an accurate time for each. This allows us to employ an optimal transport derived flow model describing transitions along the manifold, over time. It also allows us to make time resolved comparisons with a similarly built mouse gastrulation model. If you aren’t yet acquainted with the paper, please read it before jumping right in!

Please note that here we show all the single cell data as metacells. Metacells are comprised of transcriptionally similar single cells that are aggregated to form more cohesive and distinct transcriptional states (see bottom of this page for more details). For instance, this means that the time value provided for each metacell is a calculation of the mean time of the embryos from which its single cells are derived.

Where to start

On the left sidebar you will find a list of tabs, click on the tab to open it. See below a short description of each tab.

• QC : General QC and info for the dataset comprising the manifold
• Manifold : View the 2d projection of the manifold
  • Note that the manifold can be colored by gene, gene module, or metadata (such as metacell time).
  • List of top correlated (and anti-correlated) genes allows their selection for display.
• Genes : Compare gene expression and metadata over metacells.
• Markers : View a heatmap of pre-selected ‘marker genes’ over the metacell model.
• Diff. expression : Compare individual metacells / cell types, or groups of metacells selected from the 2D projection plot. Toggle the “show table” button to see the list of top differential genes.
• Cell types : View gene expression and metadata over cell types as box plots.

For any plot, single click on a ‘cell type’ from the list to toggle its appearance. Double click to isolate.

MCView

mCView creates a shiny-app facilitating interactive exploration and annotation of metacell models. Metacells itself is described here. For the latest version Metacells as used here, see

See more about MCView here, report a bug here.