Mowgli: Multi Omics Wasserstein inteGrative anaLysIs

Install the package

Mowgli is implemented as a Python package seamlessly integrated within the scverse ecosystem, in particular Muon and Scanpy.

pip install mowgli

git clone git@github.com:cantinilab/Mowgli.git
pip install ./Mowgli/

Getting started

Mowgli takes as an input a Muon object and populates its obsm and uns fiels with the embeddings and dictionaries, respectively. Visit the Getting started and API sections for more documentation and tutorials.

You may download a 10X Multiome demo dataset at https://figshare.com/s/4c8e72cbb188d8e1cce8.

from mowgli import models
import muon as mu
import scanpy as sc

# Load data into a Muon object.
mdata = mu.load_h5mu("my_data.h5mu")

# Initialize and train the model.
model = models.MowgliModel(latent_dim=15)
model.train(mdata)

# Visualize the embedding with UMAP.
sc.pp.neighbors(mdata, use_rep="W_OT")
sc.tl.umap(mdata)
sc.pl.umap(mdata)

Citation

@article{huizing2023paired,
   title={Paired single-cell multi-omics data integration with Mowgli},
   author={Huizing, Geert-Jan and Deutschmann, Ina Maria and Peyr{\'e}, Gabriel and Cantini, Laura},
   journal={Nature Communications},
   volume={14},
   number={1},
   pages={7711},
   year={2023},
   publisher={Nature Publishing Group UK London}
 }