Protomix: a Python package for ¹H-NMR metabolomics data preprocessing.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2024-11-27 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbae192

Mohammed Zniber, Youssef Fatihi, Tan-Phat Huynh

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引用次数: 0

Abstract

Motivation: NMR-based metabolomics is a field driven by technological advancements, necessitating the use of advanced preprocessing tools. Despite this need, there is a remarkable scarcity of comprehensive and user-friendly preprocessing tools in Python. To bridge this gap, we have developed Protomix-a Python package designed for metabolomics research. Protomix offers a set of automated, efficient, and user-friendly signal-preprocessing steps, tailored to streamline and enhance the preprocessing phase in metabolomics studies.

Results: This package presents a comprehensive preprocessing pipeline compatible with various data analysis tools. It encompasses a suite of functionalities for data extraction, preprocessing, and interactive visualization. Additionally, it includes a tutorial in the form of a Python Jupyter notebook, specifically designed for the analysis of 1D ¹H-NMR metabolomics data related to prostate cancer and benign prostatic hyperplasia.

Availability and implementation: Protomix can be accessed at https://github.com/mzniber/protomix and https://protomix.readthedocs.io/en/latest/index.html.

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Protomix：用于1H-NMR代谢组学数据预处理的Python包。

动机：基于核磁共振的代谢组学是一个由技术进步驱动的领域，需要使用先进的预处理工具。尽管有这种需求，但Python中缺乏全面且用户友好的预处理工具。为了弥补这一差距，我们开发了protomix -一个专门用于代谢组学研究的Python包。Protomix提供了一套自动化、高效、用户友好的信号预处理步骤，旨在简化和增强代谢组学研究中的预处理阶段。结果：该软件包提供了一个全面的预处理管道，兼容各种数据分析工具。它包含一套用于数据提取、预处理和交互式可视化的功能。此外，它还包括一个Python Jupyter笔记本形式的教程，专门用于分析与前列腺癌和良性前列腺增生相关的1D 1H-NMR代谢组学数据。可用性和实现：Protomix可以通过https://github.com/mzniber/protomix和https://protomix.readthedocs.io/en/latest/index.html访问。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量