Monkeybread: Analyze single-cell spatial transcriptomics data

About

Monkeybread is a Python package that facilitates the analysis of single-cell resolution spatial transcriptomics data such as those generated by the MERSCOPE or Xenium platforms.

Monkeybread provides tools that enable:

• Identification of cellular niches (i.e., regions with distinct compositions of cell types)
• Visualization of density of cell types across the tissue
• Statistical tests for testing for colocalization between cell types
• Statistical tests and visualiziation for ligand-receptor co-expression between neighboring cells

Monkeybread operates on datasets stored as AnnData objects and thus, can be integrated into analyses that use packages from the scverse such as scanpy or squidpy.

Monkeybread was developed at Immunitas Therapeutics.

Installation

To install Monkeybread using pip, run the following command:

pip install monkeybread

Usage

Documentation

For Monkeybread's API manual, please visit the documentation.

Tutorial

For a tutorial on running Monkeybread, please see the tutorial. This tutorial can also be run in Google Colab.