osNMF: Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology

Authors: Robert Cahill, Yu Wang, Alex Lee, Hongkui Zeng, Bin Yu, Bosiljka Tasic, Reza Abbasi-Asl

Manuscript link on BioRxiv: https://www.biorxiv.org/content/10.1101/2023.03.10.531984v1

Use

• Unsupervised identification of principal patterns (PPs) from spatial gene expression and spatial transcriptomics data
• Create of unique spatial ontologies from a search of known anatomical regions
• Stability framework to ensure stability of PPs and ontology
• Interpretabilility via gene reconstructions for each PP

Requirements

Python 3.9

Python packages: matplotlib, napari, networkx, nrrd, numpy, os, pandas, pickle, sklearn

Code

https://github.com/abbasilab/osNMF

Version

Last update: Mar 2023, v1.0

Citation

Robert Cahill, Yu Wang, Alex Lee, Hongkui Zeng, Bin Yu, Bosiljka Tasic, Reza Abbasi-Asl. Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology. bioRxiv 2023.03.10.531984; doi: https://doi.org/10.1101/2023.03.10.531984