Mellon

|zenodo| |codecov| |pypi| |conda|

.. image:: https://github.com/settylab/mellon/raw/main/landscape.png?raw=true :target: https://github.com/settylab/Mellon

Mellon is a non-parametric cell-state density estimator based on a nearest-neighbors-distance distribution. It uses a sparse gaussian process to produce a differntiable density function that can be evaluated out of sample.

Installation

To install Mellon using pip you can run:

.. code-block:: bash

pip install mellon

or to install using conda you can run:

.. code-block:: bash

conda install -c conda-forge mellon

or to install using mamba you can run:

.. code-block:: bash

mamba install -c conda-forge mellon

Any of these calls should install Mellon and its dependencies within less than 1 minute. If the dependency jax is not autimatically installed, please refer to https://github.com/google/jax.

Documentation

Please read the documentation <https://mellon.readthedocs.io/en/latest/index.html>_ or use this basic tutorial notebook <https://github.com/settylab/Mellon/blob/main/notebooks/basic_tutorial.ipynb>_.

Basic Usage

.. code-block:: python

import mellon
import numpy as np

X = np.random.rand(100, 10)  # 10-dimensional state representation for 100 cells
Y = np.random.rand(100, 10)  # arbitrary test data

model = mellon.DensityEstimator()
log_density_x = model.fit_predict(X)
log_density_y = model.predict(Y)

Citations

The Mellon manuscript is available on Nature Methods <https://www.nature.com/articles/s41592-024-02302-w> and a preprint on bioRxiv <https://www.biorxiv.org/content/10.1101/2023.07.09.548272v1>. If you use Mellon for your work, please cite our paper.

.. code-block:: bibtex

@article{ottoQuantifyingCellstateDensities2024,
  title = {Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes Using {{Mellon}}},
  author = {Otto, Dominik J. and Jordan, Cailin and Dury, Brennan and Dien, Christine and Setty, Manu},
  date = {2024-06-18},
  journaltitle = {Nature Methods},
  issn = {1548-7105},
  doi = {10.1038/s41592-024-02302-w},
  url = {https://www.nature.com/articles/s41592-024-02302-w},
}

You can find our reproducibility repository <https://github.com/settylab/MellonReproducibility> to reproduce benchmarks and plots of the paper here <https://github.com/settylab/MellonReproducibility>.

.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8404223.svg :target: https://doi.org/10.5281/zenodo.8404223 .. |codecov| image:: https://codecov.io/github/settylab/Mellon/branch/main/graph/badge.svg?token=TKIKXK4MPG :target: https://app.codecov.io/github/settylab/Mellon .. |pypi| image:: https://badge.fury.io/py/mellon.svg :target: https://badge.fury.io/py/mellon .. |conda| image:: https://anaconda.org/conda-forge/mellon/badges/version.svg :target: https://anaconda.org/conda-forge/mellon