Getting Started¶
Installation¶
This package is hosted at PyPi ( https://pypi.org/project/pypairs/ ) 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
print(result)