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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.

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

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Install SeuratWrappers

1

Install the remotes package

If you don’t already have remotes, install it from CRAN:
install.packages("remotes")
2

Install SeuratWrappers from GitHub

remotes::install_github("satijalab/seurat-wrappers")
This installs the core SeuratWrappers package. Individual method dependencies are not installed automatically.
3

Load the package

library(SeuratWrappers)

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

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CRAN packages

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

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Bioconductor packages

Several methods are distributed through Bioconductor. Install the BiocManager package first, then use it to install the relevant packages: 
install.packages("BiocManager")

BiocManager::install("batchelor")

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GitHub packages

Many wrapped methods are only available from GitHub. Install them with remotes::install_github(): 
remotes::install_github("immunogenomics/harmony")

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Per-method dependency reference

The table below lists the dependency for each wrapped method, its source, and the install command.
MethodPackageSourceInstall command
HarmonyharmonyGitHubremotes::install_github("immunogenomics/harmony")
LIGERrligerGitHubremotes::install_github("welch-lab/liger")
ConosconosGitHubremotes::install_github("hms-dbmi/conos")
fastMNNbatchelorBioconductorBiocManager::install("batchelor")
scVIPython / reticulate—See scVI method page
Monocle 3monocle3GitHubremotes::install_github("cole-trapnell-lab/monocle3")
RNA Velocityvelocyto.RGitHubremotes::install_github("velocyto-team/velocyto.R")
tricycletricycleBioconductorBiocManager::install("tricycle")
ALRAbuilt-in—No additional package required
GLM-PCAglmpcaCRANinstall.packages("glmpca")
PaCMAPPython / reticulate—See PaCMAP method page
BANKSYBanksyGitHubremotes::install_github("prabhakarlab/Banksy")
NebulosaNebulosaGitHubremotes::install_github("powellgenomicslab/Nebulosa")
miQCmiQCBioconductorBiocManager::install("miQC")
CoGAPSCoGAPSBioconductorBiocManager::install("CoGAPS")
CIPRciprGitHubremotes::install_github("atakanekiz/CIPR-Package")
PrestoprestoGitHubremotes::install_github("immunogenomics/presto")
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.

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Verify your installation

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

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

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Next steps

Introduction

Learn how SeuratWrappers works and which method categories are available.

Harmony

Start with Harmony for fast, scalable single-cell dataset integration.

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