FuseMap

Integrate spatial transcripomics with universal gene, cell, and tissue embeddings.

For more details, please check out our publication.

Manuscript code and data

Reproducibity

For code and data in the manuscript 'Towards a universal spatial molecular atlas of the mouse brain', please go to paper_code.

Exploratory analysis

We provide an interactive online database of the molCCF.

System Requirements

Hardware requirements

FuseMap package requires a standard computer with optional GPU to support the in-memory operations.

Software requirements

OS Requirements

This package is supported for Linux. The package has been tested on the following system:

• Linux: Ubuntu 20.04

Python Dependencies

FuseMap mainly depends on the Python scientific stack.

dgl
numpy
scipy
scikit-learn
pandas
pytorch
scanpy
seaborn

Installation

conda env create -f fusemap_environment.yml

Tutorial

• Read a tutorial on sample data .

Citation

If you find FuseMap useful for your work, please cite our paper:

Yichun He, Hao Sheng, Hailing Shi, Wendy Xueyi Wang, Zefang Tang, Jia Liu, Xiao Wang. Towards a universal spatial molecular atlas of the mouse brain. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/2024.05.27.594872v1 (2024).