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MELD

Project description

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Quantifying the effect of experimental perturbations in scRNA-seq data.

Note, this repository is under active development. Please check back on Monday Feb 4th 2019 for Version 0.1.

For now, check out our preprint on BioRxiv:

Enhancing experimental signals in single-cell RNA-sequencing data using graph signal processing. Daniel B Burkhardt, Jay S Stanley, Ana Luisa Perdigoto, Scott A Gigante, Kevan C Herold, Guy Wolf, Antonio Giraldez, David van Dijk, Smita Krishnaswamy. BioRxiv. doi:10.1101/532846.

Installation

pip install --user git+git://github.com/KrishnaswamyLab/MELD.git

Requirements

MELD requires Python >= 3.5. All other requirements are installed automatically by pip.

Optional

pyunlocbox is used for fast solving via proximal splitting. Install it via pip install pyunlocbox.

Usage example

import meld
import graphtools
G = graphtools.Graph(data, use_pygsp=True)
meld_score = meld.meld(label, G=G, beta=0.5)

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