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https://github.com/bebatut/pypairs

Reimplementation of the Pairs method described by A. Scialdone et al.

https://github.com/bebatut/pypairs

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Reimplementation of the Pairs method described by A. Scialdone et al.

Basic Info
  • Host: GitHub
  • Owner: bebatut
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 110 MB
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Fork of rfechtner/pypairs
Created over 7 years ago · Last pushed over 7 years ago

https://github.com/bebatut/pypairs/blob/master/ 

# PyPairs - A python scRNA-Seq classifier

This is a python-reimplementation of the _Pairs_ algorithm as described by A. Scialdone et. al. (2015).
Original Paper available under: https://doi.org/10.1016/j.ymeth.2015.06.021

The algorithm aims to classify single cells based on their transcriptomic signal. Initially created to predict cell
cycle phase from scRNA-Seq data, this algorithm can be used for various applications.

It is a supervised maschine learning algorithm and as such it consits of two components: 
training (sandbag) and prediction (cyclone)

## Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing 
purposes. 

### Installation

This package is hosted at PyPi (https://pypi.org/project/pypairs/) and can be installed on any system running Python3 
with:

```
python3 -m pip install pypairs
```

### Minimal example

Assuming you have two scRNA count files (csv, columns = samples, rows = genes) and one annotation file (csv, no header, 
two rows: "gene, class") a minimal example would look like this:

```
from pypairs import wrapper

trainings_matrix = [PATH TO MATRIX]
annotation = [PATH TO ANNOTATION]
testing_matrix = [PATH TO MATRIX]

marker_pairs = wrapper.sandbag_from_file(trainings_matrix, annotation)

prediction = wrapper.cyclone_from_file(testing_matrix, marker_pairs)
```

## Core Dependencis

* [Numpy](http://www.numpy.org/) 
* [Numba](https://numba.pydata.org/)
* [Pandas](https://pandas.pydata.org/)
* [Scanpy](https://github.com/theislab/scanpy)

## Authors

* **Antonio Scialdone** - *original algorithm*
* **Ron Fechtner** - *implementation and extension in Python*

## License 

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details

Owner

  • Name: Bérénice Batut
  • Login: bebatut
  • Kind: user
  • Location: Clermont-Ferrand, France
  • Company: University of Freiburg

@galaxyproject training, @usegalaxy-eu, @open-life-science, @StreetScienceCommunity, @gallantries

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