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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "bioIOT" in publications use:'
type: software
license: MIT
title: 'bioIOT: Inverse Optimal Transport for Single-Cell Trajectory Analysis'
version: 0.2.1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.bioIOT
abstract: '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.'
authors:
- family-names: Dong
  given-names: Han
  email: dh411424@163.com
preferred-citation:
  type: generic
  title: 'bioIOT: Inverse Optimal Transport for Single-Cell Trajectory Analysis'
  authors:
  - family-names: Dong
    given-names: Han
    email: dh411424@163.com
  year: '2026'
  notes: R package version 0.2.0
  url: https://github.com/XTSgreen/bioIOT-R
repository: https://xtsgreen.r-universe.dev
repository-code: https://github.com/XTSgreen/bioIOT-R
commit: 1efea6cda88a03941a985b8b17002432323a57d3
url: https://github.com/XTSgreen/bioIOT-R
date-released: '2026-09-04'
contact:
- family-names: Dong
  given-names: Han
  email: dh411424@163.com