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📊 🔬 Python package for normalization of gene expression matrices.

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PyGMNormalize

Normalization of gene expression matrices.

Installation

To install, run the following commands:

git clone https://github.com/ficusss/PyGMNormalize.git
cd PyGMNormalize
python setup.py install

Description

This package implements the following metods:

  • Total count normalization;
  • Percentile normalization;
  • Quartile normalization;
  • Trimmed mean of M-values normalization.

    Input data

    Each of metods takes matrix of gene expression matrix as first parameter and some method specific parameters, also some metods take optional parameter saving_memory (default saving_memory=False) for reduce the RAM usage in the calculations. Parameter matrix has genes as rows, cells as columns.

Demonstration

Demonstration of the methods is available here.

Links

  • Description of implemented methods is available here.
  • Description of "Trimmed mean of M-values" method is available here

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📊 🔬 Python package for normalization of gene expression matrices.

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