MCView creates a shiny-app facilitating interactive exploration and annotation of metacell models. Metacell itself is described here.
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.
Additional tabs can be added from the right sidebar which can be opened by clicking on the “Gears” icon at the top right of the screen. Select the tabs you want and then click on “Update Tabs”.
- QC: View QC metrics of the metacell model.
- Manifold: View the 2d projection of the manifold
- Genes: Compare gene expression and metadata over the metacells.
- Diff expression: Compare metacells / cell types.
- Markers: View a heatmap of ‘marker genes’ over the metacell model.
- Cell types: View gene expression and metadata over cell types.
- Annotate: Assign cell types and colors to metacells.
- Gene modules: Create gene modules to be used in other tabs.
Atlas projection tabs:
- Query: Examine the results of a projection of the metacell model over an atlas.
- Atlas: View the 2d projection of the atlas.
# of UMIs per metacell
Max inner-fold per metacell
# of metacells with significant inner-fold
Max inner-stdev per metacell
# of cells per metacell
Max zero-fold per metacell
# of cells with zero UMIs per gene
Projected correlation per metacell
Fitted genes per cell type