Score Velocity Genes

Score Velocity Genes produces likelihoods for the velocity genes found in an input Velocity Matrix (Image velocity_matrix_16_n_p) produced with the dynamical model. It uses groupings provided by Cell Clusters (Image cell_clusters_16_n_p) or Cell Annotations (Image cell_annotations_16_n_p).

Steady-state model: It is not possible to run the tool on a matrix produced with the steady-state model. For this, use Differential Velocity for Single Cell instead.

Note: Score Velocity Genes is complementary to Differential Velocity for Single Cell, which performs statistical tests to report p-values. Score Velocity Genes can be used to identify the genes driving the observed dynamics, either for the entire data set or a group of cells, by ranking the genes (from largest to smallest) according to the likelihood. Some genes might be equally important for two different sets of cells, without them showing differential velocity patterns.

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:

        Toolbox | Single Cell Analysis (Image sc_folder_closed_16_n_p) | Gene Expression (Image sc_gene_expression_folder_open_16_n_p) | Velocity Analysis (Image velocity_folder_open_16_n_p) | Score Velocity Genes (Image sc_diff_velocity_16_n_p)

The set set of options narrow down the focus of the tool:

For details on how groups of cells can be defined, see Differential Expression for Single Cell.

The tool outputs the gene likelihoods obtained from the dynamical model to a table (Image table_16_n_p), both for the defined groups of cells, and the entire data set. The performed calculations closely follow those from scVelo's rank_dynamical_genes method [Bergen et al., 2020].



Subsections