Reproducible computational tools, analyses, and teaching resources for trauma and tissue injury research.
CTIR 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 CTIR.
| Package | Description |
|---|---|
| bambamR | Streamlined RNA-seq analysis pipelines — from count matrices to publication-ready results |
| bamflowR | End-to-end RNA-seq and DNA-seq pipeline (STAR, BWA-MEM2, GATK, featureCounts, fastp) with a Shiny front-end |
| cellreportR | Statistical analysis and audit-ready reporting pipeline for routine cell-culture diagnostics with microscopic evaluation |
| cuvis.r | R bindings to the Cubert CUVIS SDK for reading, calibrating, and exporting hyperspectral camera data |
| dynasimR | Domain-neutral analysis and visualisation layer for discrete-event, agent-based, and node-actor simulation outputs |
| hexmakR | Generate polished hex sticker logos for R packages using customizable templates |
| 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 |
| lstparsR | Parser for NONMEM .lst output files — extracts THETA / OMEGA / SIGMA estimates into tidy data frames for population PK/PD analysis |
| molpathR | Unified molecular-pathology platform — parses NGS files (VCF, BAM, FASTQ) plus XML/PDF reports and clinical data |
| phenoscapR | Reading, QC, phenotyping, spatial statistics, and visualisation of single-cell spatial biology data from multiplexed imaging |
| 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 |
| reflowR | Custom workflowr themes and templates for reproducible research websites in R |
| 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) |
| songR | Native R/C++ implementation of SONG (Self-Organizing Nebulous Growths) for nonlinear dimensionality reduction |
Install any package with:
# install.packages("remotes")
remotes::install_github("CTTIR/<package>")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.
| 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 CTIR projects |
- Organisation website source: 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.