Package index
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check_binning() - helper function to check the input of binning
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check_valid_input() - helper function to check the inputs passed to marker detection function
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compute_observation() - Compute observation statistic for permutation framework
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compute_permp() - Calculate a p-value for correlation with permutation.
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compute_permutation() - Compute permutation statistics for permutation framework
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convert_data() - Convert SingleCellExperiment/SpatialExperiment/SpatialFeatureExperiment objects to list object for jazzPanda.
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create_genesets() - Convert the coordinates of set of genes into vectors.
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get_cluster_vectors() - Create spatial vectors for clusters
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get_gene_vectors_cm() - Create spatial vectors for genes from count matrix and cell coordinates
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get_gene_vectors_tr() - Create spatial vectors for genes from transcript coordinates
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get_lasso_coef() - help function to get lasso coefficient for every cluster for a given model
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get_vectors() - Vectorise the spatial coordinates
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lasso_markers() - Find marker genes with spatial coordinates
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rep1_clusters - Rep1 selected cells
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rep1_neg - Rep1 negative control genes within the selected region.
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rep1_sub - A small section of Xenium human breast cancer rep1.
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rep2_clusters - Rep2 selected cells
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rep2_neg - Rep2 negative control genes within the selected region.
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rep2_sub - A small section of Xenium human breast cancer rep2.