mellon

Non-parametric density inference for single-cell analysis.

https://github.com/settylab/mellon

Science Score: 67.0%

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CITATION.cff file
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✓
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DOI references
Found 5 DOI reference(s) in README
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Links to: biorxiv.org, nature.com, zenodo.org
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Low similarity (15.1%) to scientific vocabulary

Keywords

cell-differentiation density-estimation differentiable gaussian-processes single-cell

Last synced: 6 months ago · JSON representation ·

Repository

Non-parametric density inference for single-cell analysis.

Basic Info

Host: GitHub
Owner: settylab
License: gpl-3.0
Language: Jupyter Notebook
Default Branch: main
Homepage: https://mellon.readthedocs.io
Size: 20.5 MB

Statistics

Stars: 72
Watchers: 2
Forks: 4
Open Issues: 2
Releases: 14

Topics

cell-differentiation density-estimation differentiable gaussian-processes single-cell

Created over 3 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Citation

README.rst

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 `_
or use this
`basic tutorial notebook `_.


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 `_
and a preprint on
`bioRxiv `_.
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 `_
to reproduce benchmarks and plots of the paper
`here `_.


.. |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

Owner

Name: Setty Lab @ Fred Hutch
Login: settylab
Kind: organization
Location: United States of America

Website: setty-lab.org
Repositories: 4
Profile: https://github.com/settylab

We are a multi-disciplinary research group investigation differentiation trajectories using single-cell data

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Otto"
  given-names: "Dominik J."
  orcid: "https://orcid.org/0000-0002-6116-053X"
- family-names: "Jordan"
  given-names: "Cailin"
  orcid: "https://orcid.org/0000-0003-2085-3134"
- family-names: "Dury"
  given-names: "Brennan"
- family-names: "Dien"
  given-names: "Christine"
- family-names: "Setty"
  given-names: "Manu"
  orcid: "https://orcid.org/0000-0002-0344-2627"
title: "Mellon"
version: 1.3.1
doi: 10.5281/zenodo.8076507
date-released: 2023-06-24
url: "https://github.com/settylab/Mellon"
preferred-citation:
  type: article
  authors:
  - family-names: "Otto"
    given-names: "Dominik J."
    orcid: "https://orcid.org/0000-0002-6116-053X"
  - family-names: "Jordan"
    given-names: "Cailin"
    orcid: "https://orcid.org/0000-0003-2085-3134"
  - family-names: "Dury"
    given-names: "Brennan"
  - family-names: "Dien"
    given-names: "Christine"
  - family-names: "Setty"
    given-names: "Manu"
    orcid: "https://orcid.org/0000-0002-0344-2627"
  doi: 10.1038/s41592-024-02302-w
  url: "https://www.nature.com/articles/s41592-024-02302-w"
  journal: "Nature Methods"
  month: 6
  title: "Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon"
  year: 2024

GitHub Events

Total

Create event: 2
Release event: 2
Issues event: 8
Watch event: 10
Issue comment event: 19
Push event: 20
Fork event: 1

Last Year

Create event: 2
Release event: 2
Issues event: 8
Watch event: 10
Issue comment event: 19
Push event: 20
Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 9
Total pull requests: 6
Average time to close issues: 8 days
Average time to close pull requests: 9 days
Total issue authors: 9
Total pull request authors: 2
Average comments per issue: 3.44
Average comments per pull request: 0.67
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 0
Average time to close issues: 17 days
Average time to close pull requests: N/A
Issue authors: 4
Pull request authors: 0
Average comments per issue: 3.5
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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katosh (4)
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Packages

Total packages: 1
Total downloads:
- pypi 2,974 last-month

Total dependent packages: 1
Total dependent repositories: 1
Total versions: 15
Total maintainers: 1

pypi.org: mellon

Non-parametric density estimator.

Homepage: https://github.com/settylab/mellon
Documentation: https://mellon.readthedocs.io/
License: GNU General Public License v3.0
Latest release: 1.6.1
published 9 months ago

Versions: 15
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 2,974 Last month

Rankings

Downloads: 4.3%

Dependent packages count: 4.7%

Stargazers count: 13.3%

Average: 14.8%

Dependent repos count: 21.7%

Forks count: 29.8%

Maintainers (1)

katosh