> ## Documentation Index
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> Use this file to discover all available pages before exploring further.

# ReadAlevin()

> Import alevin quantification output into a Seurat object

`ReadAlevin()` reads the output of the alevin salmon quantification tool and creates a Seurat object with the resulting count matrix.

## Syntax

```r theme={null}
ReadAlevin(
  file,
  getMeta = FALSE,
  meanAndVariance = FALSE,
  ...
)
```

## Parameters

<ParamField path="file" type="character" required>
  Path to the alevin output directory or quant.sf file.
</ParamField>

<ParamField path="getMeta" type="logical" default="FALSE">
  If `TRUE`, uses `tximeta` instead of `tximport` to load data with genomic range metadata (requires `tximeta` to be installed). When successful, gene-level metadata (chromosome, start, end) is added to the assay.
</ParamField>

<ParamField path="meanAndVariance" type="logical" default="FALSE">
  If `TRUE`, loads the alevin mean and variance matrices instead of counts. The mean matrix becomes the `counts` slot and the variance matrix becomes the `data` slot.
</ParamField>

<ParamField path="..." type="any">
  Additional parameters passed to `tximport::tximport()` or `tximeta::tximeta()`.
</ParamField>

## Returns

A Seurat object created from the alevin count matrix. When `getMeta = TRUE` and genomic ranges are available, the assay includes `chr`, `start`, and `end` feature-level metadata.

## Prerequisites

```r theme={null}
BiocManager::install(c("tximport", "fishpond"))
# Optional for metadata:
BiocManager::install("tximeta")
```

## Examples

```r theme={null}
library(SeuratWrappers)
BiocManager::install(c("tximport", "fishpond"))

# Basic import
object <- ReadAlevin(file = "alevin/output/dir")

# Import with genomic metadata
object <- ReadAlevin(file = "alevin/output/dir", getMeta = TRUE)

# Access genomic ranges
head(object[["RNA"]][[c("chr", "start", "end")]])

# Continue with standard Seurat workflow
object <- NormalizeData(object)
object <- FindVariableFeatures(object)
```

## See Also

* [Alevin method guide](/methods/alevin)
* Reference: Srivastava et al., Genome Biology 2019