Reproducible computational tools, analyses, and teaching resources for trauma and tissue injury research.
CTTIR develops open-source software, reproducible analysis pipelines, and educational materials at the interface of trauma surgery, tissue injury, and computational biomedicine. Our work spans biomarker discovery, multi-modal imaging, dimensionality reduction, molecular pathology, and clinical-translational data science.
Statistical and analytical R packages developed and maintained by CTTIR, grouped by theme.
Status ●●● published · ●●○ usable · ●○○ draft · ○○○ idea
| Package | Status | DOI | Description |
|---|---|---|---|
| annotatR | ●●○ | -na- | Multi-layer region-of-interest annotation for whole-slide microscopy, hyperspectral cubes, and rasters — exports binary, labelled, and multi-class masks (GeoJSON, QuPath, TIFF) with a resumable Shiny/OpenSeadragon batch annotator |
| cellreportR | ●●○ | -na- | Statistical analysis and audit-ready reporting pipeline for routine cell-culture diagnostics with microscopic evaluation |
| phenoscapR | ●●○ | -na- | Reading, QC, phenotyping, spatial statistics, and visualisation of single-cell spatial biology data from multiplexed imaging |
| scimagR | ●●○ | -na- | End-to-end pipeline for longitudinal MRI/CT analysis in spinal-cord injury research (wraps Spinal Cord Toolbox, dcm2niix) |
| segmantR | ●●○ | -na- | Cell segmentation for histology and multiplexed tissue imaging with human-in-the-loop training (classical + Cellpose/StarDist/Mesmer) |
| Package | Status | DOI | Description |
|---|---|---|---|
| cuvis.r | ●●○ | -na- | R bindings to the Cubert CUVIS SDK for reading, calibrating, and exporting hyperspectral camera data |
| hyperspectR | ●●○ | -na- | Complete pipeline for biomedical hyperspectral imaging — from raw camera data to clinical tissue oxygenation maps |
| libscanR | ●●○ | -na- | Vendor-agnostic analysis and visualisation of Laser-Induced Breakdown Spectroscopy (LIBS) data, with a biomedical-tissue focus |
| Package | Status | DOI | Description |
|---|---|---|---|
| bambamR | ●●○ | -na- | Streamlined RNA-seq analysis pipelines — from count matrices to publication-ready results |
| Package | Status | DOI | Description |
|---|---|---|---|
| molpathR | ●●○ | -na- | Unified molecular-pathology platform — parses NGS files (VCF, BAM, FASTQ) plus XML/PDF reports and clinical data |
| zhncommandR | ●●○ | -na- | Auditor live-evaluation dashboard for haematological oncology cohorts — quality/coverage indicators, OPS-coded complex-therapy and diagnostics counts, Kaplan–Meier, oncoprint, and cytogenetics summaries in an interactive Shiny app |
| Package | Status | DOI | Description |
|---|---|---|---|
| harbouR | ●●○ | -na- | Unofficial R client for the SeaTable REST API — read, write, and sync collaborative cloud databases from R |
| lstparsR | ●●○ | -na- | Parser for NONMEM .lst output files — extracts THETA / OMEGA / SIGMA estimates into tidy data frames for population PK/PD analysis |
| pressR | ●●○ | -na- | Parsing, analysis, and visualisation of capacitive pressure-distribution data (insoles, saddles, seating, pedography) |
| qviewparsR | ●●● |  |
Pure-R parser for the binary .Q-View project format used in chemiluminescent multiplex ELISA plate imaging |
| Package | Status | DOI | Description |
|---|---|---|---|
| dynasimR | ●●○ | -na- | Domain-neutral analysis and visualisation layer for discrete-event, agent-based, and node-actor simulation outputs |
| scimapR | ●●○ | -na- | Reproducible, question-driven, embedding-aware science mapping — bibliometric and scientometric analysis toolkit |
| songR | ●●○ | -na- | Native R/C++ implementation of SONG (Self-Organizing Nebulous Growths) for nonlinear dimensionality reduction |
| Package | Status | DOI | Description |
|---|---|---|---|
| hexmakR | ●●○ | -na- | Generate polished hex sticker logos for R packages using customizable templates |
| reflowR | ●●○ | -na- | Custom workflowr themes and templates for reproducible research websites in R |
| themakR | ●●○ | -na- | Shared pkgdown template giving the CTTIR package suite a unified look — Hugo Coder palette with a light/dark toggle |
Install any package with:
# install.packages("remotes")
remotes::install_github("CTTIR/<package>")Standalone apps and tools that complement the R package suite.
Status ●●● published · ●●○ usable · ●○○ draft · ○○○ idea
| Application | Status | DOI | Description |
|---|---|---|---|
| pwa-quest | ●●○ | -na- | Offline-first Progressive Web App for collecting questionnaire responses in research and field settings — exports sessions as QR codes or CSV / XLSX / TXT / XML |
| shinylaunchR | ●●○ | -na- | Cross-platform desktop launchpad for R/Shiny apps — opens packaged apps, Shiny files, or hosted URLs each in its own native window while R runs headless |
Plugins that extend Zotero for curated, reproducible reference management.
Status ●●● published · ●●○ usable · ●○○ draft · ○○○ idea
| Plugin | Status | DOI | Description |
|---|---|---|---|
| argus-one | ●●○ | -na- | Merges duplicate Zotero items by DOI only — keeps the newest record's fields, unions collections, tags, and attachments inside one transaction |
| attaclone-dedup | ●●○ | -na- | Detects and resolves duplicate file attachments by content hash — auto-removes byte-identical bare copies, prompts a review dialog for annotated PDFs |
| metadata-mender | ●●○ | -na- | Reconciles and completes item metadata against PubMed, OpenAlex, Crossref, Semantic Scholar, OpenAIRE, Unpaywall, CORE, and CRAN |
Install by downloading the .xpi from the corresponding repository's Releases page, then Tools → Plugins → ⚙ → Install Plugin From File… in Zotero.
| Repository | Description |
|---|---|
| courses | Course materials taught by the group |
| tutorials | Hands-on tutorials accompanying our packages and methods |
| Repository | Description |
|---|---|
| ressources | Shared assets, references, and supporting material used across CTTIR projects |
- Organisation website: cttir.github.io/website — source at CTTIR/website
Most repositories carry an MIT license and a CITATION.cff file. Please cite the specific package or repository you use — see each repo's README.md for the canonical citation.
For questions, contributions, or collaboration enquiries, open an issue on the relevant repository.