Differential Velocity for Single Cell
Differential Velocity for Single Cell performs differential analysis from an input Velocity Matrix () and groupings provided by Cell Clusters () or Cell Annotations ().
Note: Differential Velocity for Single Cell is complementary to Score Velocity Genes, which reports likelihoods. Differential Velocity for Single Cell performs statistical tests to report p-values and identify genes that show different velocity patterns in between groups of cells. |
It is often most natural to run the tool from a Dimensionality Reduction Plot by right-clicking on the plot, see UMAP and tSNE plot functionality for details. However, it can also be found in the Toolbox here:
Gene Expression () | Velocity Analysis () | Differential Velocity for Single Cell ()
The tool performs a differential analysis for the velocity of each gene and outputs Statistical Comparison Tables ().
The available options specify the type of test to be performed and how genes can be filtered before testing, in a similar manner as for Differential Expression for Single Cell; see Differential Expression for Single Cell for details. Note that Differential Velocity for Single Cell can only run an 'Identify marker genes' analysis and the 'All group pairs' option is not available.
The tool performs pairwise comparisons by using the estimated velocities for each gene to calculate:
- Max group mean. The maximum of the average velocities of the two groups. Can be negative.
- Fold change. The (signed) fold change, calculated as the ratio between the average velocities of the two groups. Note that if one group has a positive average, while the other group has a negative average, the fold change is reported as NaN (not a number).
- P-value. The p-value is obtained from a Mann-Whitney U test (also known as Wilcoxon rank-sum test).
See Interpreting the output of Differential Expression for Single Cell for more details on the output and Differential Expression for Single Cell for details on how the pairwise comparisons are used to 'Identify marker genes'.