ficusss / PyGMNormalize

:bar_chart: :microscope: Python package for normalization of gene expression matrices.

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