Voyager

Abstract

1. Introduction

The companion website for this package includes vignettes that showcase the functionality of Voyager in the context of the Visium, Slide-seq V2, CosMx, Xenium, and MERFISH technologies.

This package brings the tradition of geospatial statistics to spatial omics by wrapping classical geospatial packages such as spdep and gstat to be used with the SpatialFeatureExperiment class, which extends SpatialExperiment with sf.

2. Objective

From geospatial to spatial -omics

This project demonstrates how R can be applied to a real-world Data Science problem.

4. Technology Stack

5. System Requirements

General requirements for this technology stack — check the README for exact versions.

• See the project README for exact requirements
• Git (to clone the repository)

6. Installation & Setup

git clone https://github.com/pachterlab/voyager.git
cd voyager

if (!requireNamespace("BiocManager")) install.packages("BiocManager")
BiocManager::install(version = "3.17") # Or a higher version in the future
BiocManager::install("Voyager")

# install.packages("remotes")
remotes::install_github("pachterlab/voyager", ref = "devel")

BiocManager::install("Voyager", version = "devel")

Full setup instructions are in the project README.

7. Future Enhancements

Suggested extensions you can add to make this your own project.

• Turn the analysis into an interactive dashboard
• Automate data refresh with a scheduled job
• Add a predictive model on top of the analysis

8. Viva / Review Questions

Common questions examiners ask for projects in this domain.

1. What is the source of the dataset and how was missing data handled?
2. Which exploratory analysis steps revealed the most useful insight?
3. Why were these particular charts chosen to present the data?
4. Which statistical or ML technique supports the conclusions?
5. How could the analysis be automated or refreshed with new data?

9. Source Code & License

This project is developed by pachterlab and published on GitHub under the Artistic License 2.0. Please follow the license terms and credit the original author when you use or modify this code.