Package: bioIOT 0.2.1

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.

Authors:Han Dong [aut, cre]

bioIOT_0.2.1.tar.gz
bioIOT_0.2.1.zip(r-4.7-any)bioIOT_0.2.1.zip(r-4.6-any)bioIOT_0.2.1.zip(r-4.5-any)
bioIOT_0.2.1.tgz(r-4.6-any)bioIOT_0.2.1.tgz(r-4.5-any)
bioIOT_0.2.1.tar.gz(r-4.7-any)bioIOT_0.2.1.tar.gz(r-4.6-any)
bioIOT_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bioIOT/json (API)

# Install 'bioIOT' in R:

install.packages('bioIOT', repos = c('https://xtsgreen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/xtsgreen/bioiot-r/issues

Datasets:

demo_iot_states - Bundled bioIOT demo dataset

On CRAN:

bioinformatics optimal-transport pseudotime single-cell trajectory-inference

4.00 score 2 stars 21 exports 17 dependencies

Last updated from:1efea6cda8. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	277
source / vignettes	OK	271
linux-release	OK	215
macos-release	OK	198
macos-oldrel	OK	215
windows-devel	OK	138
windows-release	OK	147
windows-oldrel	OK	144
wasm-release	OK	167

Exports:build_state_features collapse_probes find_platform_file fit_iot gsm_id has_cel_file make_cost pathway_markers plot_pathway_trend plot_theta plot_transition_flow plot_transition_heatmap pseudotime_from_transition row_ce_loss row_conditional runIOT score_pathways simulate_iot_states soft_sinkhorn transition_matrix zscore_phi

Dependencies:cli cpp11 farver ggplot2 glue gtable isoband labeling lifecycle R6 RColorBrewer rlang S7 scales vctrs viridisLite withr

bioIOT quickstart

Rendered frombioIOT.Rnwusingutils::Sweave

Last update: 2026-09-04
Started: 2026-09-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Collapse a probe-level expression matrix to gene level	collapse_probes
Bundled bioIOT demo dataset	demo_iot_states
Fit inverse optimal transport feature weights	fit_iot print.bioIOT_fit summary.bioIOT_fit
Extract GSM ids from CEL filenames	gsm_id
Cost construction, likelihood and feature standardization	make_cost row_ce_loss zscore_phi
IOT pathway marker genes (8 pathways)	pathway_markers
bioIOT visualisation	plot_pathway_trend plot_theta plot_transition_flow plot_transition_heatmap
Run IOT on a single-cell object	runIOT runIOT.default runIOT.matrix runIOT.Seurat runIOT.SingleCellExperiment
Score bulk-cohort samples on the 8 IOT pathways	score_pathways
Simulate single-cell state-transition data for bioIOT	simulate_iot_states
Semi-relaxed OT solver and row-conditional transitions	row_conditional soft_sinkhorn
Inspect a GEO RAW tar without extracting	find_platform_file has_cel_file
Transition matrix, pseudotime and state features	build_state_features pseudotime_from_transition transition_matrix