Filtering optionsFilter cells based on total UMI count.
Mitochodrial RNA OptionsEnter a regular expression to define the subset of mitochondrial. (e.g. ^mt- for mouse or ^MT- for human. Leave blank to skip this analysis.
Filter cells based on percentage of mitochondrial RNA.
Sampling optionsRandomly sample a subset of cells passing filters. This allows for quicker exploration, before using the full dataset.
Plot showing total UMI per barcode. Barcodes selected for further analysis are displayed in green.
Violin plots showing distributions of total UMI per cell, and number of detected genes per cell.
Histogram of mean gene expression across all cells.
Variable Genes Options
Identify features that are outliers on a 'mean variability plot'.
Select the set of genes to use and the number of principal components to compute.
Differential Expression OptionsSelect options for marker gene discovery.
Heatmap showing gene expression for the top markers in each cluster.