MetaAnalyst: a user-friendly tool for metagenomic biomarker detection and phenotype classification

BMC Medical Research Methodology

Software

Abdullah Hayajneh¹  Erchin Serpedin¹  Ammar Gharaibeh²  Mustafa Alshawaqfeh²  Salahelden Rababah³ 

[1] Electrical and Computer Engineering Department, Texas A &M University, College Station, TX, USA;School of Electrical Engineering and Information Technology, German Jordanian University, Amman, Jordan;School of Electrical Engineering and Information Technology, German Jordanian University, Amman, Jordan;Department of Systems Science and Industrial Engineering, State University of New York at Binghamton, Binghamton, NY, USA;

关键词: Metagenomics;    Biomarker detection;    Phenotype classification;    Graphical user interface;    Software;   

DOI  :  10.1186/s12874-022-01812-5

 received in 2022-07-24, accepted in 2022-11-28,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundMany metagenomic studies have linked the imbalance in microbial abundance profiles to a wide range of diseases. These studies suggest utilizing the microbial abundance profiles as potential markers for metagenomic-associated conditions. Due to the inevitable importance of biomarkers in understanding the disease progression and the development of possible therapies, various computational tools have been proposed for metagenomic biomarker detection. However, most existing tools require prior scripting knowledge and lack user friendly interfaces, causing considerable time and effort to install, configure, and run these tools. Besides, there is no available all-in-one solution for running and comparing various metagenomic biomarker detection simultaneously. In addition, most of these tools just present the suggested biomarkers without any statistical evaluation for their quality.ResultsTo overcome these limitations, this work presents MetaAnalyst, a software package with a simple graphical user interface (GUI) that (i) automates the installation and configuration of 28 state-of-the-art tools, (ii) supports flexible study design to enable studying the dataset under different scenarios smoothly, iii) runs and evaluates several algorithms simultaneously iv) supports different input formats and provides the user with several preprocessing capabilities, v) provides a variety of metrics to evaluate the quality of the suggested markers, and vi) presents the outcomes in the form of publication quality plots with various formatting capabilities as well as Excel sheets.ConclusionsThe utility of this tool has been verified through studying a metagenomic dataset under four scenarios. The executable file for MetaAnalyst along with its user manual are made available at https://github.com/mshawaqfeh/MetaAnalyst.

【 授权许可】

CC BY   
© The Author(s) 2022

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