All functions |
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Joint dimension reduction and spatial clustering |
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Joint dimension reduction and spatial clustering |
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tNSE or UMAP plot visualization |
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Find spatially variable genes |
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Generate simulated data |
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Calculate the adjacency matrix given the spatial coordinates |
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Calculate adjacency matrix by automatically choosing radius |
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Calculate adjacency matrix by user-specified radius |
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getneighborhood_fast |
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A human dorsolateral prefrontal cortex data |
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MBIC plot visualization |
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Read the spatial transcriptomics data measured on 10X Visium platform |
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Read the scRNAseq data measured on scRNA sequencing platform |
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Run Weighted Principal Component Analysis |
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Select the number of clusters |
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Spatial coordinates plot visualization |
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Calculate column-wise or row-wise mean |
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Calculate column-wise or row-wise sum |
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Return the top n SVGs |