stana: an R package for metagenotyping analysis and interactive application based on clinical data

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Metagenotyping is crucial for resolving microbial intraspecies diversity via single nucleotide variants.
• Gene copy number analysis enhances understanding of microbial community metabolic functions.
• A lack of integrated platforms hinders the analysis of metagenotyping results with relevant grouping data.

Purpose of the Study:

• To develop an R package, stana, for processing and analyzing metagenotyping data.
• To provide an interactive environment for exploring metagenotyping results.
• To facilitate the study of gut microbiome metagenotypes in relation to human diseases.

Main Methods:

• Development of the R package 'stana' with modules for preprocessing, statistical analysis, functional analysis, and visualization.
• Creation of an interactive analysis environment.
• Utilized over 1000 publicly available metagenome samples related to human diseases.

Main Results:

• The stana package enables comprehensive analysis of metagenotyping data, including variant identification and gene copy number assessment.
• An interactive environment was released, integrating over 1000 human disease-related metagenome samples.
• Analysis of gut microbiome metagenotypes in end-stage renal disease, Crohn's disease, and Parkinson's disease was performed.

Conclusions:

• The stana package effectively supports the analysis of metagenotyping data, confirming previous findings and generating new hypotheses.
• The developed platform facilitates deeper insights into the link between microbial communities and human diseases.
• The R package and interactive environment are publicly available for research use.