SeuratExtendData

Data package for SeuratExtend containing reference databases and datasets.

Overview

SeuratExtendData provides:

1. Gene Ontology (GO) Databases: Pre-processed GO annotation data for human and mouse
2. Reactome Pathway Databases: Processed Reactome pathway data for human and mouse
3. Gene Set Collections: Additional curated gene sets including Hallmark 50 and others

Version Information

SeuratExtendData is periodically updated to include the latest reference databases:

• v0.3.0 (April 2025): Contains updated GO and Reactome databases from April 2025
• v0.2.1 (January 2020): Contains the original stable databases

Users who need reproducible results may wish to install a specific version. This can be done using the install_SeuratExtendData() function from SeuratExtend:

# Install the latest version with most recent databases
SeuratExtend::install_SeuratExtendData("latest")

# Install the stable version (January 2020 databases)
SeuratExtend::install_SeuratExtendData("stable") 

Creating Custom Databases

For users who need the most recent database versions or want to work with custom organisms, SeuratExtendData provides tools to create and use custom databases:

1. Gene Ontology (GO): Create custom GO databases from OBO and GAF files
2. Reactome: Create custom Reactome databases from Reactome data dumps

The detailed documentation for creating and using custom databases is available in the following guides:

• Creating GO Data
• Creating Reactome Data

These guides contain step-by-step instructions for downloading the latest files, processing them, and using the resulting databases with SeuratExtend.

Using Custom Databases with SeuratExtend

After creating custom database files, you can use them with SeuratExtend as follows:

# Load your custom GO data
custom_GO_Data <- readRDS("path/to/your/GO_Data.rds")

# Replace the default database with your custom one
original_GO_Data <- SeuratExtendData::GO_Data
assignInNamespace("GO_Data", custom_GO_Data, ns = "SeuratExtendData")

# Run your analysis
seu <- GeneSetAnalysisGO(seu, parent = "immune_system_process")

# Optionally restore the original database afterward
assignInNamespace("GO_Data", original_GO_Data, ns = "SeuratExtendData")

A similar approach can be used for custom Reactome databases.

Installation

The package is automatically installed as a dependency of SeuratExtend. If you need to install it separately:

if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")
}
remotes::install_github("huayc09/SeuratExtendData")