Package index
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check_binning()
- helper function to check the input of binning
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check_geneset_input()
- helper function to check the inputs passed to create geneset function
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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.