Projects
Research themes pursued by CTTIR. Each project card brings together the relevant Software packages and the Workflows that demonstrate them in practice — the full path from method development to applied analysis on a defined research question.
Software cards live at Software. End-to-end demonstrations live at Workflows.
Single-Cell Analysis
Cellular composition and state in injured and healthy tissue. CTTIR develops methods and software for end-to-end single-cell analysis — from raw counts through QC, embedding, segmentation-aware spatial context, and publication-ready cell-level reporting.
- Single-Cell Tissue Atlas
- Multi-Modal Tissue Integration (includes single-cell)
Hyperspectral Imaging
Label-free tissue characterization from spectral signatures. CTTIR develops HSI ingest, preprocessing, library matching, and interpretable embedding methods for tissue-region classification, with reproducible reporting baked in.
hyperspectR— HSI cube ingest and preprocessinglibscanR— reference-spectrum library matchingannotatR— labelling regions of interest on spectral cubessongR— interpretable embeddings over spectral featuresreflowR— CTTIR-styled reproducible report themes
Cross-Modal Integration
Aligning high-dimensional modalities — imaging, single-cell, bulk omics, multiplex protein, molecular pathology — into a coherent translational view. CTTIR's flagship integration theme: methods and software for harmonizing heterogeneous data into shared representations, with cohort-level inference and interactive exploration. Connects assay-level processing to translational inference end-to-end.
hyperspectR— modality-specific ingest and processingcellreportR— cell-level reportingbambamR— bulk RNA-seq processingsegmantR— segmentation utilitiesannotatR— cross-modal region-of-interest annotationscimagR— single-cell imaging integrationqviewparsR— multiplex protein parsingpressR— cohort reportingmolpathR— molecular pathology cohort assembly and interactive explorationzhncommandR— haematological-oncology cohort audit dashboardsongR— joint interpretable embeddings across modalitiesdynasimR— synthetic ground truth for integration benchmarking
Basic Bioinformatics
Foundational methods, benchmarking, and reproducibility infrastructure. The methodological backbone of CTTIR's applied work: interpretable dimensionality reduction, RNA-seq fundamentals, simulation-based benchmarking, and reproducible reporting templates that the applied projects build on.