{"entity":{"id":"spagcn","kind":"term","name":"Spatially aware clustering (SpaGCN, KNN smoothing)","aka":["SpaGCN","spatially aware clustering","spatial clustering","neighbour-smoothed PCA","KNN neighbourhood smoothing","KNN smoothing","graph convolutional clustering"],"tldr":"Spatially aware clustering groups the spots of a tissue section into domains using both what they express and where they sit, so the domains are contiguous regions rather than scattered spots.","summary":"SpaGCN, from Hu and colleagues, uses a graph convolutional network over spots linked by spatial proximity and histology to identify spatial domains and their marker genes. Simpler versions average each spot with its k nearest neighbours (Wikipedia on k-NN) before principal components and k-means clustering (Wikipedia), which reduces the sparsity of spatial counts and yields coherent regions at the cost of blurring boundaries. Moran's I then tests whether the resulting labels or risk scores are spatially structured.","asOf":"2026-09-24","links":[{"label":"Hu et al., SpaGCN: integrating gene expression, spatial location and histology to identify spatial domains (Nature Methods 2021)","url":"https://doi.org/10.1038/s41592-021-01255-8"},{"label":"SpaGCN on GitHub","url":"https://github.com/jianhuupenn/SpaGCN"},{"label":"Wikipedia: k-nearest neighbours","url":"https://en.wikipedia.org/wiki/K-nearest_neighbors_algorithm"},{"label":"Wikipedia: k-means clustering","url":"https://en.wikipedia.org/wiki/K-means_clustering"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":["spatial-transcriptomics"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["spatial-autocorrelation","pca","spatial-transcriptomics-platforms"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/spagcn."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Methods and models"},"route":"/terms/spagcn/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"pca","kind":"term","name":"Principal component analysis (PCA) as a feature compressor","route":"/terms/pca/"},{"id":"spatial-autocorrelation","kind":"term","name":"Spatial autocorrelation (Moran's I)","route":"/terms/spatial-autocorrelation/"},{"id":"spatial-transcriptomics-platforms","kind":"term","name":"Spatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX)","route":"/terms/spatial-transcriptomics-platforms/"}],"technology":[{"id":"spatial-transcriptomics","kind":"technology","name":"Spatial transcriptomics","route":"/technologies/spatial-transcriptomics/"}]}}