https://github.com/ficusss/PyGMNormalize

:bar_chart: :microscope: Python package for normalization of gene expression matrices.
https://github.com/ficusss/PyGMNormalize

Last synced: 23 days ago
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:bar_chart: :microscope: Python package for normalization of gene expression matrices.

• Host: GitHub
• URL: https://github.com/ficusss/PyGMNormalize
• Owner: ficusss
• License: mit
• Created: 2017-10-06T20:48:35.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2019-11-30T00:47:11.000Z (over 4 years ago)
• Last Synced: 2024-02-24T14:31:12.115Z (4 months ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 1.05 MB
• Stars: 9
• Watchers: 3
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome_single_cell - PyGMNormalize - [Python] - Python implementation of [edgeR](https://www.ncbi.nlm.nih.gov/pubmed/19910308) normalization method for count matrices. (Software packages / RNA-seq)
• awesome-single-cell - PyGMNormalize - [Python] - Python implementation of [edgeR](https://www.ncbi.nlm.nih.gov/pubmed/19910308) normalization method for count matrices. (Software packages / RNA-seq)
• awesome-single-cell - PyGMNormalize - [Python] - Python implementation of [edgeR](https://www.ncbi.nlm.nih.gov/pubmed/19910308) normalization method for count matrices. (Software packages / RNA-seq)

README

        
# 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](https://github.com/ficusss/PyGMNormalize/blob/master/notebooks/demonstration.ipynb).

## Links

- Description of implemented methods is available [here](https://www.hindawi.com/journals/bmri/2015/621690/).

- Description of "Trimmed mean of M-values" method is available [here](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-3-r25)