Software

Streamlined RNA-seq analysis pipelines — from count matrices to publication-ready results.

Statistical analysis and audit-ready reporting pipeline for routine cell-culture diagnostics with microscopic evaluation.

R bindings to the Cubert CUVIS SDK for reading, calibrating, and exporting hyperspectral camera data.

Domain-neutral analysis and visualisation layer for discrete-event, agent-based, and node-actor simulation outputs.

Unofficial R client for the SeaTable REST API — read, write, and sync collaborative cloud databases from R.

Generate polished hex sticker logos for R packages using customizable templates.

Complete R pipeline for biomedical hyperspectral imaging — from raw camera data to clinical tissue oxygenation maps.

Vendor-agnostic analysis and visualisation of Laser-Induced Breakdown Spectroscopy (LIBS) data, with a focus on biomedical tissue applications.

Parser for NONMEM .lst output files — extracts THETA / OMEGA / SIGMA estimates into tidy data frames for population PK/PD analysis.

Unified R platform for molecular pathology data — parses NGS files (VCF, BAM, FASTQ), XML/PDF reports, and clinical data into a queryable database with an interactive Shiny app.

Reading, QC, phenotyping, spatial statistics, and visualisation of single-cell spatial biology data from multiplexed imaging platforms.

Parsing, analysis, and visualisation of capacitive pressure-distribution data — insoles, saddles (equine and bicycle), seating, and barefoot pedography.

Pure-R parser for the binary .Q-View project file format used in chemiluminescent multiplex ELISA plate imaging and quantification.

Custom workflowr themes and templates for reproducible research websites in R.

End-to-end R pipeline for longitudinal MRI and CT analysis in spinal-cord injury research (wraps Spinal Cord Toolbox, dcm2niix, pydicom).

Reproducible, question-driven, embedding-aware science mapping — a toolkit for bibliometric and scientometric analysis.

Cell segmentation for histology and multiplexed tissue imaging with human-in-the-loop training — classical methods plus Cellpose, StarDist, and Mesmer.

Native R/C++ implementation of SONG (Self-Organizing Nebulous Growths) for nonlinear dimensionality reduction and visualisation.

Shared pkgdown template giving the CTTIR package suite a unified look — Hugo Coder palette with a light/dark toggle.

Merges duplicate Zotero items by DOI only — keeps the newest record's fields, unions collections, tags, and attachments inside one transaction.

Detects and resolves duplicate file attachments by content hash — auto-removes byte-identical bare copies, prompts a review dialog for annotated PDFs.

Reconciles and completes item metadata against PubMed, OpenAlex, Crossref, Semantic Scholar, OpenAIRE, Unpaywall, CORE, and CRAN.

Offline-first Progressive Web App for collecting questionnaire responses in research and field settings — exports sessions as QR codes or CSV / XLSX / TXT / XML.