Vesalius

Welcome to the Vesalius GitHub page!

What is Vesalius ?

Vesalius is an R package to decipher tissue anatomy by embracing various image analysis techniques for high-resolution ST data. Vesalius identifies spatially expressed genes linked to the morphology of tissue structures.

How to install Vesalius?

Vesalius requires R 4.0.0 or higher. The list of dependencies can be found in the DESCRIPTION FILE.

If you do not have devtools already installed, please do so beforehand.

install.packages("devtools")

Ensure that the library has been loaded

library(devtools)

Install Vesalius via GitHub

install_github("WonLab-CS/Vesalius")

How to use Vesalius?

Vesalius provides an internal data set taken from real Spatial Transcriptomic data. This can be used as a dummy data set to get a feel for the Vesalius workflow. The run time on this data sets should not exceed a minute.

The "Quick Start" guide can be found here

Further in depth examples can be found in the Vesalius Analysis Page

Vesalius has been tested on:

• macOS Sequoia 15.0
• Red Hat Enterprise Linux 8.5 (Ootpa)

What's next?

The Vesalius package is in its early stage of development. We would ask you to share with us any bugs, concerns, or features you wish to see implemented.

Please open a GitHub issue or send an email to Patrick Martin ([email protected] - [email protected])

Archived Analysis

An in depth view of the Vesalius workflow related to the MSB manuscript can be found here.