scMMDI 0.0.1

A deep learning framework for single cell multimode data mosaic integration

scMMDI_py

scMMDI: A deep learning framework for single cell multimode data mosaic integration This is the Python implementation of the scMMDI algorithm. Note that this implementation supports GPU acceleration.

1. Installation

You can use the following command to install scMMDI:

pip install scMMDI

2. Usage

scMMDI accepts a muon object as input and populates the obsm and uns fields with embeddings and dictionaries, respectively. The pre-processed PBMC dataset is available for download here. It is recommended that a GPU be used to run the model. To initialize and run the scMMDI model, the following code should be used:

from scMMDI.model import scMMDI
import mudata as md
import scanpy as sc

# Load data into a Muon object.
mdata = md.read_h5mu("my_data.h5mu")

# Initialize and train the model.
model = scMMDI(latent_dim=30)
model.fit(mdata)

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

'scMMDI' class also has other methods, you can use the 'help' or '?' command for more details explanations of the methods.