Filtering options
Filter cells based on total UMI count.Mitochodrial RNA Options
Enter 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 options
Randomly 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.
Filtering summary:
Options
Histogram of mean gene expression across all cells.
Variable Genes Options
Identify features that are outliers on a 'mean variability plot'.
PCA Options
Select the set of genes to use and the number of principal components to compute.
Clustering Options
t-SNE Options
Differential Expression Options
Select options for marker gene discovery.
Heatmap showing gene expression for the top markers in each cluster.
Generate report