spiky

spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with synthetic spike-in standard oligos to enable quantitative comparison of samples across subjects, experiments, and time points in both relative and absolute terms.

Key Features:

• Spike-in calibration: Uses synthetic spike-in standard oligos as controls for cfMeDIP experiments.
• Cross-sample quantification: Enables quantitative comparison of diagnostic results across specimens, subjects, and experiments.
• Absolute and relative quantification: Supports both relative and absolute quantitative comparisons across time points.

Scientific Applications:

• Liquid biopsy diagnostics: Facilitates cfMeDIP-based diagnostics for non-invasive analysis using cell-free DNA without destructive conversion of scarce template.
• Longitudinal monitoring: Allows tracking of methylation patterns across multiple time points in clinical or experimental settings.

Methodology:

spiky implements methods and model generation for cfMeDIP with spike-in controls; specific computational steps are not detailed in the sources.