Getting Started


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

Datasets provide a example scRNA dataset and default marker pairs for cell cycle prediction:

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