This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
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This project identifies haematopoietic progenitor-niche interactions in developing tissues (skin and bone marrow) and compares them to tumor-niche interactions in skin-infiltrating leukaemias. Newly generated single cell RNA sequencing data, Visium and Xenium spatial transcriptomics data will be combined with published data. Analysis will use published tools implemented in python and R, for example cell-cell interaction analysis, trajectory analysis, NMF-based niche detection and infer CNV.
This research will primarily use computational methods for single-cell RNA sequencing and spatial transcriptomics analysis using the Python and R scientific computing ecosystems. Core libraries will include scanpy, anndata, Seurat, numpy, pandas, scipy and matplotlib for data processing, statistical analysis and visualisation. Published computational tools will be applied for cell-cell interaction analysis, developmental trajectory analysis, niche detection, spatial organisation analysis and copy-number variation inference to compare normal developmental programmes with tumour-associated microenvironmental interactions.