FuseSOM - A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets
A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (`FuseSOM`) is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by combining a `Self Organizing Map` architecture and a `Multiview` integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays.
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singlecellcellbasedassaysclusteringspatial
4.89 score 1 stars 26 scripts 397 downloads
PACE - Proximity-Associated Changes in Expression for Spatial Transcriptomics
PACE (Proximity-Associated Changes in Expression) is a hierarchical empirical Bayes framework that quantifies how a cell's gene expression changes with proximity to specific neighbouring cell types in imaging-based spatial transcriptomics such as Xenium and CosMx. It fits negative binomial mixed models with partial pooling across cell types, corrects for transcript contamination between adjacent cells with a per-cell ambient term, and decomposes expression variance into cell-type identity, spatial cell state, contamination, and residual components. Input and output follow SpatialExperiment conventions.
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spatialtranscriptomicsgeneexpressionsinglecellregressionbayesiandifferentialexpressionsoftwarecpp
3.85 score 5 scripts