Own software
R · R package (v0.1.0)
An R package for structural and practical identifiability of PK/PD ODE models built on rxode2: which parameters can be determined from given outputs and doses, how precisely a sampling design would estimate them, and whether likelihood profiles of nlmixr2 fits are bounded or flat.
Ten reference models with expected results fixed from the literature or by derivation are reproduced, and two independent structural methods agree at every point. Expected standard errors agreed with the spread of repeated estimates on simulated data. R CMD check passes on Linux and Windows in CI (October 5, 2026). Decisions are local; population designs are not covered.
GitHub · Usage · Release 0.1.0
R · R package and CLI (v0.1.1)
An R package and command-line tool that turns RSEM *.genes.results files and an ordinary sample metadata table into standard bulk RNA-seq results as TSV tables: expression summaries, normalization, PCA, sample correlation, DESeq2 differential expression for an explicitly stated design, preranked GSEA, GSVA/ssGSEA scores and gene annotation.
Human and mouse data. Mismatched samples, inconsistent gene tables, missing model values and confounded designs stop the run instead of producing results. Simple effects from interaction models are tested against the reparameterized model. On ENCODE K562 knockdown data, each target gene is among the most significant decreases in its own knockdown. R CMD check passes on Linux, macOS and Windows in CI (October 6, 2026). Not on CRAN or Bioconductor; no figures are produced.
GitHub · Documentation · Get started · Installation · Tutorial · Release 0.1.1
R · R package (v0.1.0)
A small, dependency-free R companion to reticulate that reports Python selection overrides and project markers before Python starts, for diagnosing why managed requirements from py_require() are not used.
Initial version, not on CRAN. R package checks pass in CI on Linux, Windows and macOS (October 5, 2026). It reports visible hints and does not reproduce reticulate's own discovery; use reticulate's diagnostics for actual configuration.
GitHub · Usage
R · Research code
R scripts exploring transformations of compositional time series and dynamic interaction inference using CCM (Convergent Cross Mapping), including simulations and figure-generation code.
All six figure scripts parsed, and a small CCM example using original functions ran with legacy rEDM 0.7.3 on October 3, 2026. A reproduction README and automated smoke check are provided. Complete figure analyses have not been rerun.
GitHub
Python · Prototype
A Python CLI connecting marker-gene discovery and extraction from genomes with alignment, sequence concatenation, and phylogenetic inference.
Invocation, failure handling and marker-alignment validation are implemented. Nine smoke tests passed locally and in Linux CI on October 3, 2026. Installed CLI execution was checked; the complete phylogenetic workflow with external tools remains unvalidated.
GitHub · Usage
Docker / Shell · Tutorial (Japanese)
A Japanese-language tutorial with Shell scripts for Docker-based shotgun metagenomic analysis, covering quality control and functional profiling.
Scripts now check inputs, references and existing outputs, stop on tool failures, and retain diagnostic files. Eight local control-flow tests passed on October 3, 2026; automated Linux checks are configured. Full real-data Docker analysis remains unvalidated.
GitHub · Tutorial (Japanese)
Docker · Analysis environments
Dockerfiles for running existing bioinformatics tools in containers, including genome and metagenome analysis environments.
MAFFT and SeqKit environments were refreshed and passed Docker builds plus small FASTA execution checks in Linux CI on October 3, 2026. Other environment definitions remain historical and unverified.
GitHub
