> ## 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.

# Installation

> Install SeuratWrappers and the per-method dependencies required for the wrappers you plan to use.

## Prerequisites

Before installing SeuratWrappers, make sure your environment meets the following requirements:

* **R >= 3.5.0** — check with `R.version` in your R console
* **Seurat >= 5.0.0** — install from CRAN with `install.packages("Seurat")`
* **remotes** — used to install packages from GitHub

<Note>
  SeuratWrappers wraps methods that are distributed separately. The core SeuratWrappers package is lightweight; each wrapped method requires its own package, installed independently.
</Note>

## Install SeuratWrappers

<Steps>
  <Step title="Install the remotes package">
    If you don't already have `remotes`, install it from CRAN:

    ```r theme={null}
    install.packages("remotes")
    ```
  </Step>

  <Step title="Install SeuratWrappers from GitHub">
    ```r theme={null}
    remotes::install_github("satijalab/seurat-wrappers")
    ```

    This installs the core SeuratWrappers package. Individual method dependencies are **not** installed automatically.
  </Step>

  <Step title="Load the package">
    ```r theme={null}
    library(SeuratWrappers)
    ```
  </Step>
</Steps>

## Install method dependencies

Each wrapper depends on the underlying method's R package, which must be installed separately. You only need to install the packages for the methods you plan to use.

<Tip>
  If you call a wrapper function without the required dependency installed, SeuratWrappers will prompt you interactively and offer to install the missing package automatically.
</Tip>

### CRAN packages

Some dependencies are available on CRAN and can be installed with `install.packages()`:

```r theme={null}
# glmpca
install.packages("glmpca")
```

### Bioconductor packages

Several methods are distributed through [Bioconductor](https://bioconductor.org). Install the `BiocManager` package first, then use it to install the relevant packages:

```r theme={null}
install.packages("BiocManager")
```

<CodeGroup>
  ```r fastMNN (batchelor) theme={null}
  BiocManager::install("batchelor")
  ```

  ```r CoGAPS theme={null}
  BiocManager::install("CoGAPS")
  ```

  ```r tricycle theme={null}
  BiocManager::install("tricycle")
  ```

  ```r miQC theme={null}
  BiocManager::install("miQC")
  ```
</CodeGroup>

### GitHub packages

Many wrapped methods are only available from GitHub. Install them with `remotes::install_github()`:

<CodeGroup>
  ```r Harmony theme={null}
  remotes::install_github("immunogenomics/harmony")
  ```

  ```r LIGER theme={null}
  remotes::install_github("welch-lab/liger")
  ```

  ```r Monocle 3 theme={null}
  remotes::install_github("cole-trapnell-lab/monocle3")
  ```

  ```r Conos theme={null}
  remotes::install_github("hms-dbmi/conos")
  ```

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

  ```r BANKSY theme={null}
  remotes::install_github("prabhakarlab/Banksy")
  ```

  ```r Nebulosa theme={null}
  remotes::install_github("powellgenomicslab/Nebulosa")
  ```

  ```r CIPR theme={null}
  remotes::install_github("atakanekiz/CIPR-Package")
  ```
</CodeGroup>

## Per-method dependency reference

The table below lists the dependency for each wrapped method, its source, and the install command.

| Method       | Package             | Source       | Install command                                         |
| ------------ | ------------------- | ------------ | ------------------------------------------------------- |
| Harmony      | `harmony`           | GitHub       | `remotes::install_github("immunogenomics/harmony")`     |
| LIGER        | `rliger`            | GitHub       | `remotes::install_github("welch-lab/liger")`            |
| Conos        | `conos`             | GitHub       | `remotes::install_github("hms-dbmi/conos")`             |
| fastMNN      | `batchelor`         | Bioconductor | `BiocManager::install("batchelor")`                     |
| scVI         | Python / reticulate | —            | See [scVI method page](/methods/scvi)                   |
| Monocle 3    | `monocle3`          | GitHub       | `remotes::install_github("cole-trapnell-lab/monocle3")` |
| RNA Velocity | `velocyto.R`        | GitHub       | `remotes::install_github("velocyto-team/velocyto.R")`   |
| tricycle     | `tricycle`          | Bioconductor | `BiocManager::install("tricycle")`                      |
| ALRA         | built-in            | —            | No additional package required                          |
| GLM-PCA      | `glmpca`            | CRAN         | `install.packages("glmpca")`                            |
| PaCMAP       | Python / reticulate | —            | See [PaCMAP method page](/methods/pacmap)               |
| BANKSY       | `Banksy`            | GitHub       | `remotes::install_github("prabhakarlab/Banksy")`        |
| Nebulosa     | `Nebulosa`          | GitHub       | `remotes::install_github("powellgenomicslab/Nebulosa")` |
| miQC         | `miQC`              | Bioconductor | `BiocManager::install("miQC")`                          |
| CoGAPS       | `CoGAPS`            | Bioconductor | `BiocManager::install("CoGAPS")`                        |
| CIPR         | `cipr`              | GitHub       | `remotes::install_github("atakanekiz/CIPR-Package")`    |
| Presto       | `presto`            | GitHub       | `remotes::install_github("immunogenomics/presto")`      |

<Warning>
  Some GitHub packages (such as `velocyto.R` and `conos`) have system-level dependencies, such as a C++ compiler and Boost libraries. If installation fails, check the package's README for platform-specific instructions.
</Warning>

## Verify your installation

After installing, confirm that SeuratWrappers loads correctly and that the dependency for your chosen method is available:

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

# Check that a specific dependency is installed
# Example: verify harmony is available
requireNamespace("harmony", quietly = TRUE)
#> [1] TRUE
```

## Next steps

<Columns cols={2}>
  <Card title="Introduction" icon="book-open" href="/introduction">
    Learn how SeuratWrappers works and which method categories are available.
  </Card>

  <Card title="Harmony" icon="layer-group" href="/methods/harmony">
    Start with Harmony for fast, scalable single-cell dataset integration.
  </Card>
</Columns>