Inverse Optimal Transport for Single-Cell Trajectory Analysis R package bioIOT version 0.2.2 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. Software Depends: R (>= 4.0.0) Imports: utils, ggplot2 Suggests: testthat (>= 3.0.0), knitr, rmarkdown, SingleCellExperiment, Seurat, SummarizedExperiment, S4Vectors Han Dong <dh411424@163.com> Comprehensive R Archive Network (CRAN) Han Dong [aut, cre] (Nickname: XTSgreen) MIT + file LICENSE (https://CRAN.R-project.org/package=bioIOT/LICENSE) 2026-09-24 application/tgz https://CRAN.R-project.org/package=bioIOT doi:10.32614/CRAN.package.bioIOT