DspikeIn

DspikeIn provides a reproducible and modular workflow for absolute microbial quantification using spike-in controls with user-defined spike-in volumes and genome copy numbers.

Key Features:

• Spike-in Support: Supports both single spike-in taxa and synthetic microbial communities with user-defined spike-in volumes and genome copy numbers.
• Data Structure Compatibility: Compatible with 'phyloseq' and 'TreeSummarizedExperiment' (TSE) data structures.
• Spike-in Validation: Implements methods for spike-in validation.
• Preprocessing: Implements methods for preprocessing.
• Scaling Factor Estimation: Implements methods for scaling factor estimation.
• Absolute Abundance Conversion: Implements methods for absolute abundance conversion.
• Bias Correction: Implements methods for bias correction.
• Normalization: Implements methods for normalization.
• Downstream Statistical Analysis: Facilitates downstream statistical analyses with 'DESeq2', 'edgeR', and other Bioconductor-compatible methods.
• Visualization: Visualization tools are provided via 'ggplot2', 'ggtree', and related packages.

Scientific Applications:

• Absolute Microbial Quantification: Enables absolute microbial quantification using spike-in controls for microbial community analysis.
• Downstream Differential Abundance Analysis: Supports downstream statistical analyses with 'DESeq2', 'edgeR', and other Bioconductor-compatible methods.

Methodology:

The package implements methods for spike-in validation, preprocessing, scaling factor estimation, absolute abundance conversion, bias correction, and normalization.