Usage

Installation

You can install Pronoms directly from PyPI using pip:

pip install pronoms

Basic Usage

import numpy as np
from pronoms.normalizers import (
    MedianNormalizer,
    QuantileNormalizer,
    L1Normalizer,
    VSNNormalizer
)

# Example data: 5 samples (rows) and 3 proteins (columns)
data = np.array([
    [10, 20, 30],
    [15, 25, 35],
    [20, 30, 40],
    [25, 35, 45],
    [30, 40, 50]
])

# Median normalization
med_norm = MedianNormalizer()
med_data = med_norm.normalize(data)

# Quantile normalization
qnorm = QuantileNormalizer()
q_data = qnorm.normalize(data)

# L1 normalization
l1norm = L1Normalizer()
l1_data = l1norm.normalize(data)

# VSN normalization (requires R and Bioconductor 'vsn' package)
vsn_norm = VSNNormalizer()
vsn_data = vsn_norm.normalize(data)

See each normalizer’s documentation for detailed API and parameters.