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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.
| Version: | 0.2.2 |
| Depends: | R (≥ 4.0.0) |
| Imports: | utils, ggplot2 |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown, SingleCellExperiment, Seurat, SummarizedExperiment, S4Vectors |
| Published: | 2026-09-24 |
| DOI: | 10.32614/CRAN.package.bioIOT (may not be active yet) |
| Author: | Han Dong [aut, cre] (Nickname: XTSgreen) |
| Maintainer: | Han Dong <dh411424 at 163.com> |
| BugReports: | https://github.com/XTSgreen/bioIOT-R/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/XTSgreen/bioIOT-R |
| NeedsCompilation: | no |
| Citation: | bioIOT citation info |
| Materials: | README, NEWS |
| CRAN checks: | bioIOT results |
| Reference manual: | bioIOT.html , bioIOT.pdf |
| Vignettes: |
bioIOT quickstart (source, R code) |
| Package source: | bioIOT_0.2.2.tar.gz |
| Windows binaries: | r-devel: not available, r-release: bioIOT_0.2.2.zip, r-oldrel: bioIOT_0.2.2.zip |
| macOS binaries: | r-release (arm64): bioIOT_0.2.2.tgz, r-oldrel (arm64): bioIOT_0.2.2.tgz, r-release (x86_64): bioIOT_0.2.2.tgz, r-oldrel (x86_64): bioIOT_0.2.2.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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