Breast Cancer |https://anthbapt.github.io/tags/breast-cancer/Breast CancerHugoBlox Kit (https://hugoblox.com)en-usWed, 01 Oct 2025 00:00:00 +0000https://anthbapt.github.io/media/icon_hu_da05098ef60dc2e7.pngBreast Cancerhttps://anthbapt.github.io/tags/breast-cancer/SMART: A Spatio-Molecular Atlas of Response Trajectories in Triple-Negative Breast Cancerhttps://anthbapt.github.io/publications/smart-tnbc-2025/Wed, 01 Oct 2025 00:00:00 +0000https://anthbapt.github.io/publications/smart-tnbc-2025/METABRIC-MXhttps://anthbapt.github.io/projects/metabric-mx/Sat, 01 Jun 2024 00:00:00 +0000https://anthbapt.github.io/projects/metabric-mx/<p>METABRIC-MX (Multimodal eXplorer) is a platform for processing and analysing Xenium breast cancer spatial transcriptomics data from the METABRIC cohort. The pipeline handles:</p> <ul> <li><strong>Multi-modal registration</strong>: Aligning metallomics, immunofluorescence, H&amp;E, and Xenium data into unified SpatialData/Zarr objects</li> <li><strong>Cell typing</strong>: Automated annotation using CellTypist with the Chen.pkl model trained on 600k+ cells</li> <li><strong>Batch correction</strong>: Harmony and scVI integration across tissue microarray cores</li> <li><strong>Spatial analysis</strong>: KNN smoothing, neighbourhood composition, and immune niche profiling</li> </ul>