microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization

Autor:	Yang Cao, Qingyang Dong, Dan Wang, Pengcheng Zhang, Ying Liu, Chao Niu
Rok vydání:	2022
Předmět:	Statistics and Probability Computational Mathematics Computational Theory and Mathematics Microbiota Molecular Biology Biochemistry Software Biomarkers Computer Science Applications
Zdroj:	Bioinformatics. 38:4027-4029
ISSN:	1367-4811 1367-4803
DOI:	10.1093/bioinformatics/btac438
Popis:	Summary Characterizing biomarkers based on microbiome profiles has great potential for translational medicine and precision medicine. Here, we present microbiomeMarker, an R/Bioconductor package implementing commonly used normalization and differential analysis (DA) methods, and three supervised learning models to identify microbiome markers. microbiomeMarker also allows comparison of different methods of DA and confounder analysis. It uses standardized input and output formats, which renders it highly scalable and extensible, and allows it to seamlessly interface with other microbiome packages and tools. In addition, the package provides a set of functions to visualize and interpret the identified microbiome markers. Availability and implementation microbiomeMarker is freely available from Bioconductor (https://www.bioconductor.org/packages/microbiomeMarker). Source code is available and maintained at GitHub (https://github.com/yiluheihei/microbiomeMarker). Supplementary information Supplementary data are available at Bioinformatics online.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::10db9d794835cce65981ae32e5b76e92 https://doi.org/10.1093/bioinformatics/btac438 Zobrazit plný text záznamu