> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/satijalab/seurat-wrappers/llms.txt
> Use this file to discover all available pages before exploring further.

# RunVelocity()

> Estimate RNA velocity from spliced and unspliced count matrices

`RunVelocity()` estimates RNA velocity by comparing spliced and unspliced RNA counts, storing the result in the Seurat object's `Tool` slot for downstream visualization.

## Syntax

```r theme={null}
RunVelocity(
  object,
  spliced = "spliced",
  unspliced = "unspliced",
  ambiguous = NULL,
  spliced.average = 0.2,
  unspliced.average = 0.05,
  reduction = "pca",
  group.by = "ident",
  cells = NULL,
  graph = NULL,
  ncores = 1,
  verbose = TRUE,
  ...
)
```

## Parameters

<ParamField path="object" type="Seurat" required>
  A Seurat object with spliced and unspliced assays loaded (e.g., via `ReadVelocity()` + `as.Seurat()`).
</ParamField>

<ParamField path="spliced" type="character" default="spliced">
  Name of the assay containing spliced RNA counts.
</ParamField>

<ParamField path="unspliced" type="character" default="unspliced">
  Name of the assay containing unspliced RNA counts.
</ParamField>

<ParamField path="ambiguous" type="character" default="NULL">
  Optional name of the assay containing ambiguous RNA counts.
</ParamField>

<ParamField path="spliced.average" type="numeric" default="0.2">
  Minimum required average expression in the spliced matrix for a gene to be included.
</ParamField>

<ParamField path="unspliced.average" type="numeric" default="0.05">
  Minimum required average expression in the unspliced matrix for a gene to be included.
</ParamField>

<ParamField path="reduction" type="character" default="pca">
  Name of the reduction to use for computing the embedding distance matrix.
</ParamField>

<ParamField path="group.by" type="character" default="ident">
  Metadata column to use for grouping cells when filtering genes.
</ParamField>

<ParamField path="cells" type="character vector" default="NULL">
  Specific cells to include. Defaults to all cells.
</ParamField>

<ParamField path="graph" type="character" default="NULL">
  Name of a nearest-neighbor graph to use. If `NULL`, one is computed from the reduction.
</ParamField>

<ParamField path="ncores" type="integer" default="1">
  Number of CPU cores for parallel computation.
</ParamField>

<ParamField path="..." type="any">
  Additional parameters passed to `velocyto.R::gene.relative.velocity.estimates()`.
</ParamField>

## Returns

A Seurat object with velocity estimates stored in `Tool(object)`. Use `velocyto.R::show.velocity.on.embedding.cor()` to visualize the velocity field on a 2D embedding.

## Examples

```r theme={null}
library(SeuratWrappers)
remotes::install_github("velocyto-team/velocyto.R")

# Read velocity data from loom file
ldat <- ReadVelocity(file = "sample.loom")
object <- as.Seurat(ldat)

# Preprocess and run velocity
DefaultAssay(object) <- "spliced"
object <- SCTransform(object, assay = "spliced")
object <- RunPCA(object)
object <- RunVelocity(
  object = object,
  reduction = "pca",
  ncores = 8,
  verbose = TRUE
)

# Visualize
ident.colors <- setNames(palette(), levels(Idents(object)))
velocyto.R::show.velocity.on.embedding.cor(
  emb = Embeddings(object, reduction = "umap"),
  vel = Tool(object = object, slot = "RunVelocity"),
  n = 200,
  scale = "sqrt",
  cell.colors = ident.colors[Idents(object)]
)
```

## See Also

* [`ReadVelocity()`](/api/read-velocity)
* [RNA Velocity method guide](/methods/velocity)