> ## 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.

# ExportToCellbrowser()

> Export a Seurat object to UCSC Cell Browser format for interactive visualization

`ExportToCellbrowser()` exports a Seurat object as a UCSC Cell Browser dataset. It creates all required files (expression matrix, metadata, cell embeddings, marker genes) in the specified directory and optionally launches a local Cell Browser server.

## Syntax

```r theme={null}
ExportToCellbrowser(
  object,
  dir,
  dataset.name = Project(object = object),
  reductions = NULL,
  markers.file = NULL,
  cluster.field = NULL,
  cb.dir = NULL,
  port = NULL,
  use.mtx = FALSE,
  meta.fields = NULL,
  meta.fields.names = NULL,
  matrix.slot = "counts",
  markers.n = 100,
  skip.markers = FALSE,
  skip.expr.matrix = FALSE,
  skip.metadata = FALSE,
  skip.reductions = FALSE
)
```

## Parameters

<ParamField path="object" type="Seurat" required>
  A Seurat object to export.
</ParamField>

<ParamField path="dir" type="character" required>
  Output directory where Cell Browser files will be written.
</ParamField>

<ParamField path="dataset.name" type="character">
  Name of the Cell Browser dataset. Defaults to `Project(object)`.
</ParamField>

<ParamField path="reductions" type="character vector" default="NULL">
  Names of dimensional reductions to export. If `NULL`, exports all available reductions.
</ParamField>

<ParamField path="markers.file" type="character" default="NULL">
  Path to a pre-computed markers file. If `NULL` and `skip.markers = FALSE`, markers are computed automatically.
</ParamField>

<ParamField path="cluster.field" type="character" default="NULL">
  Metadata column to use as cell cluster labels.
</ParamField>

<ParamField path="cb.dir" type="character" default="NULL">
  If provided, also builds the Cell Browser HTML in this directory for direct serving.
</ParamField>

<ParamField path="port" type="integer" default="NULL">
  If provided, launches a local Cell Browser server on this port after export.
</ParamField>

<ParamField path="use.mtx" type="logical" default="FALSE">
  Export the expression matrix in `.mtx.gz` format (sparse). Automatically enabled for very large matrices.
</ParamField>

<ParamField path="meta.fields" type="character vector" default="NULL">
  Metadata columns to include. If `NULL`, all metadata columns are exported.
</ParamField>

<ParamField path="meta.fields.names" type="character vector" default="NULL">
  Display names for the metadata fields specified in `meta.fields`.
</ParamField>

<ParamField path="matrix.slot" type="character" default="counts">
  Which expression matrix to export. One of `"counts"`, `"data"`, or `"scale.data"`.
</ParamField>

<ParamField path="markers.n" type="integer" default="100">
  Number of top markers per cluster to include in the exported markers file.
</ParamField>

<ParamField path="skip.markers" type="logical" default="FALSE">
  Skip marker gene computation and export.
</ParamField>

<ParamField path="skip.expr.matrix" type="logical" default="FALSE">
  Skip expression matrix export (for incremental updates).
</ParamField>

<ParamField path="skip.metadata" type="logical" default="FALSE">
  Skip metadata export.
</ParamField>

<ParamField path="skip.reductions" type="logical" default="FALSE">
  Skip dimensional reduction export.
</ParamField>

## Returns

Invisibly returns `NULL`. Creates the following files in `dir`:

* `exprMatrix.tsv.gz` (or `matrix.mtx.gz`) — expression matrix
* `meta.tsv` — cell metadata
* `<reduction>.coords.tsv.gz` — cell coordinates for each reduction
* `markers.tsv` — marker genes per cluster
* `cellbrowser.conf` — Cell Browser configuration file

## StopCellbrowser()

Stops a running Cell Browser server started by `ExportToCellbrowser()`.

```r theme={null}
StopCellbrowser()
```

## Examples

```r theme={null}
library(SeuratWrappers)

# Export only
ExportToCellbrowser(
  object = seurat_obj,
  dir = "cellbrowser_output",
  dataset.name = "PBMC_3k"
)

# Export and launch local server on port 8080
ExportToCellbrowser(
  object = seurat_obj,
  dir = "cellbrowser_output",
  dataset.name = "PBMC_3k",
  cb.dir = "cellbrowser_html",
  port = 8080
)

# Stop the server when done
StopCellbrowser()
```

## See Also

* [Cell Browser method guide](/methods/cellbrowser)