SimSpace documentation

πŸ‘‹ Welcome to SimSpace Documentation

SimSpace is a flexible and extensible simulation framework for generating spatial omics data with customizable spatial structures, cell types, and gene expression profiles. It supports both reference-free and reference-based simulation modes, allowing users to create diverse tissue architectures ranging from well-defined niches to spatially intermixed environments across resolutions. Moreover, SimSpace also supports three-dimensional simulations, capturing the full complexity of tissue structure.

This documentation covers:

  • βœ… Installation instructions (Python & R environments)

  • πŸ§ͺ Tutorials for reference-free and reference-based simulation

  • πŸ›  API Reference for all SimSpace modules and functions

πŸ“¦ Installation

To install the latest version of SimSpace, we recommend using conda to setup the environment:

git clone https://github.com/TianxiaoNYU/simspace.git

  • Create a conda environment for simspace

cd simspace
conda env create -f environment.yml
conda activate simspace

  • Install simspace from PyPi

pip install simspace

🧬 Optional: Setting Up the R Environment for Omics Simulation

SimSpace supports external omics profile simulation via R-based tools, including scDesign3, SRTsim, and splatter. These tools are optional but recommended if you want to simulate gene expression profiles in addition to spatial patterns.

To enable this functionality, please install the required R packages manually in your system R environment:

Steps:

  • Ensure that R (version 4.4 or compatible) is installed on your system. You can download it from CRAN.

  • Open an R session and install the required packages:

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("SONGDONGYUAN1994/scDesign3")
devtools::install_github("xzhoulab/SRTsim")

if (!require("devtools", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("splatter"))

Once installed, SimSpace will automatically use these tools when relevant R-based simulations are requested.

Tutorials

API Reference