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@CTTIR

CTIR

Computational Trauma and Tissue Injury Research
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Computational Trauma and Tissue Injury Research

Reproducible computational tools, analyses, and teaching resources for trauma and tissue injury research.

Website · Tutorials · Courses · Resources

About

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.

R Packages

Statistical and analytical R packages developed and maintained by CTTIR, grouped by theme.

Imaging & Microscopy

Package Description
annotatR 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 Statistical analysis and audit-ready reporting pipeline for routine cell-culture diagnostics with microscopic evaluation
phenoscapR Reading, QC, phenotyping, spatial statistics, and visualisation of single-cell spatial biology data from multiplexed imaging
scimagR End-to-end pipeline for longitudinal MRI/CT analysis in spinal-cord injury research (wraps Spinal Cord Toolbox, dcm2niix)
segmantR Cell segmentation for histology and multiplexed tissue imaging with human-in-the-loop training (classical + Cellpose/StarDist/Mesmer)

Spectral & Hyperspectral

Package Description
cuvis.r R bindings to the Cubert CUVIS SDK for reading, calibrating, and exporting hyperspectral camera data
hyperspectR Complete pipeline for biomedical hyperspectral imaging — from raw camera data to clinical tissue oxygenation maps
libscanR Vendor-agnostic analysis and visualisation of Laser-Induced Breakdown Spectroscopy (LIBS) data, with a biomedical-tissue focus

Omics & Transcriptomics

Package Description
bambamR Streamlined RNA-seq analysis pipelines — from count matrices to publication-ready results

Clinical & Molecular Pathology

Package Description
molpathR Unified molecular-pathology platform — parses NGS files (VCF, BAM, FASTQ) plus XML/PDF reports and clinical data
zhncommandR 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

Parsers & Data I/O

Package Description
harbouR Unofficial R client for the SeaTable REST API — read, write, and sync collaborative cloud databases from R
lstparsR Parser for NONMEM .lst output files — extracts THETA / OMEGA / SIGMA estimates into tidy data frames for population PK/PD analysis
pressR 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

Methods & Analytics

Package Description
dynasimR Domain-neutral analysis and visualisation layer for discrete-event, agent-based, and node-actor simulation outputs
scimapR Reproducible, question-driven, embedding-aware science mapping — bibliometric and scientometric analysis toolkit
songR Native R/C++ implementation of SONG (Self-Organizing Nebulous Growths) for nonlinear dimensionality reduction

Reproducibility & Tooling

Package Description
hexmakR Generate polished hex sticker logos for R packages using customizable templates
reflowR Custom workflowr themes and templates for reproducible research websites in R
themakR 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>")

Applications

Standalone apps and tools that complement the R package suite.

Application Description
pwa-quest 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 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

Zotero Plugins

Plugins that extend Zotero for curated, reproducible reference management.

Plugin Description
argus-one Merges duplicate Zotero items by DOI only — keeps the newest record's fields, unions collections, tags, and attachments inside one transaction
attaclone-dedup Detects and resolves duplicate file attachments by content hash — auto-removes byte-identical bare copies, prompts a review dialog for annotated PDFs
metadata-mender 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.

Tutorials & Courses

Repository Description
courses Course materials taught by the group
tutorials Hands-on tutorials accompanying our packages and methods

Resources

Repository Description
ressources Shared assets, references, and supporting material used across CTTIR projects

Web Presence

Contributing & Citation

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.

Maintained by the CTTIR group · github.com/CTTIR

Popular repositories Loading

  1. songR songR Public

    R package for SONG dimensionality reduction — structured, interpretable embeddings for high-dimensional biological data

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  2. bambamR bambamR Public

    R package for streamlined RNA-seq analysis pipelines — from count matrices to publication-ready results

    R 1

  3. phenoscapR phenoscapR Public

    R package for analyzing and visualizing single-cell spatial data

    R 1

  4. hexmakR hexmakR Public

    R package for generating polished hex sticker logos for R packages using customizable templates

    R

  5. reflowR reflowR Public

    Custom workflowr themes and templates for reproducible research websites in R

    R

  6. molpathR molpathR Public

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

    R

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