multivelovae 0.1.0

Velocity inference from multi-lineage, multi-omic, and multi-sample single-cell data

MultiVeloVAE - Velocity inference from multi-lineage, multi-omic, and multi-sample single-cell data

Package Installation

The package depends on several popular packages in computational biology and machine learning, including scanpy, scVelo, PyTorch, and scikit-learn. We suggest using a GPU to accelerate the training process.

To install the MultiVeloVAE package through PyPI:

pip install multivelovae

And import the package inside python:

import multivelovae as vv

Package Usage

Please feel free to test this method on our previously published 10X Multiome datasets. See https://multivelo.readthedocs.io/en/latest/MultiVelo_Demo.html. The example of running the mouse brain dataset is located in paper-notebooks. Alternatively, you can apply the same training and analysis steps on our single-sample HSPC dataset for which we provide the AnnData objects directly in figshare. Expected runtimes can be found inside each notebook.

This file lists the versions of packages used to generate manuscript figures.

TODO

bioconda readthedocs