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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:

A supervised maschine learning algorithm aiming 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.

Build to be fully compatible with Scanpy. For more details see the full documentation.

Getting Started

Note: Version 3 still under development.


This package is hosted at PyPi ( ) and can be installed on any system running Python3 via pip with:

pip install pypairs

Alternatively, pypairs can be installed using Conda (most easily obtained via the Miniconda Python distribution:

conda install -c bioconda 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 pairs, datasets

# Load samples from the oscope scRNA-Seq dataset with known cell cycle
training_data = datasets.leng15(mode='sorted')

# Run sandbag() to identify marker pairs
marker_pairs = pairs.sandbag(training_data, fraction=0.6)

# Load samples from the oscope scRNA-Seq dataset without known cell cycle
testing_data = datasets.leng15(mode='unsorted')

# Run cyclone() score and predict cell cycle classes
result = pairs.cyclone(testing_data, marker_pairs)

# Further downstream analysis

Core Dependencies


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


This project is licensed under the BSD 3-Clause License - see the LICENSE file for details