bioIOT - Inverse Optimal Transport for Single-Cell Trajectory Analysis

Semi-relaxed inverse optimal transport ('IOT') for single-cell state-transition and 'pseudotime' analysis: a self-contained R solver (Anderson-accelerated soft 'Sinkhorn' with exact implicit gradients), feature-weight fitting with a two-stage bias-corrected refit and multi-restart, state transition matrices, random-walk 'pseudotime', 'ggplot2' visualisation, soft-gated Seurat and 'SingleCellExperiment' interfaces, reproducible simulated demo data, and bulk-cohort pathway scoring utilities.