Projects
Research themes pursued by CTIR. 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. CTIR 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.
cellreportR— publication-ready cell-level reportsscimagR— single-cell imaging integrationsegmantR— segmentation utilitiesbambamR— bulk reference profiles for calibrationsongR— interpretable embeddings
- Single-Cell Tissue Atlas
- Multi-Modal Tissue Integration (includes single-cell)
Hyperspectral Imaging
Label-free tissue characterization from spectral signatures. CTIR 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 matchingsongR— interpretable embeddings over spectral featuresreflowR— CTIR-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. CTIR'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 utilitiesscimagR— single-cell imaging integrationqviewparsR— multiplex protein parsingpressR— cohort reportingmolpathR— molecular pathology cohort assembly and interactive explorationsongR— joint interpretable embeddings across modalitiesdynasimR— synthetic ground truth for integration benchmarking
Basic Bioinformatics
Foundational methods, benchmarking, and reproducibility infrastructure. The methodological backbone of CTIR's applied work: interpretable dimensionality reduction, RNA-seq fundamentals, simulation-based benchmarking, and reproducible reporting templates that the applied projects build on.