tidyMicro

tidyMicro provides an R-based pipeline for processing high-dimensional sequence count tables and associated metadata, performing diversity inference, exploratory and longitudinal visualizations (including Rocky Mountain plots and longitudinal ordination plots), and regression modeling (negative binomial, beta binomial, and rank-based tests) to analyze microbial community composition and dynamics.

Key Features:

• Tidyverse integration: Maintains tidyverse-compatible data structures for microbiome datasets within R.
• Comprehensive data management: Handles high-dimensional sequence count tables and integrates taxonomic or functional gene/pathway counts with study metadata.
• Diversity and exploratory analyses: Implements standard exploratory visualizations and diversity inference tools for community assessment.
• Regression modeling: Provides advanced regression options including negative binomial, beta binomial, and rank-based testing methods.
• Specialized visualizations: Generates Rocky Mountain plots and longitudinal ordination plots for temporal and comparative community analyses.

Scientific Applications:

• Ecological studies: Characterizes microbial community composition and dynamics in ecological research.
• Environmental monitoring: Analyzes microbiome shifts for environmental assessment and monitoring.
• Health sciences: Supports microbiome investigations related to human, animal, or clinical studies.
• General microbiome research: Applies to any research area requiring analysis of taxonomic or functional gene/pathway count data.

Methodology:

Processes high-dimensional sequence count tables, integrates them with study metadata, performs diversity inference and exploratory visualizations, applies negative binomial, beta binomial, and rank-based regression tests, and produces Rocky Mountain and longitudinal ordination plots while maintaining tidyverse-compatible data structures in R.