Package: bioIOT
Type: Package
Title: Inverse Optimal Transport for Single-Cell Trajectory Analysis
Version: 0.2.2
Authors@R: person(given = "Han", family = "Dong", role = c("aut", "cre"),
    email = "dh411424@163.com", comment = c(Nickname = "XTSgreen"))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: utils, ggplot2
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, SingleCellExperiment,
        Seurat, SummarizedExperiment, S4Vectors
URL: https://github.com/XTSgreen/bioIOT-R
BugReports: https://github.com/XTSgreen/bioIOT-R/issues
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-09-14 15:40:40 UTC; XTS-green
Author: Han Dong [aut, cre] (Nickname: XTSgreen)
Maintainer: Han Dong <dh411424@163.com>
Repository: CRAN
Date/Publication: 2026-09-24 13:40:24 UTC
