Package index
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Seurat5obj_to_SpaTopic() - Convert a Seurat v5 object as the input of 'SpaTopic'
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SpaTopicSpaTopic-packageSpaTopic-Package - SpaTopic: Spatial Topic Modeling for Multiplexed Images
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SpaTopic-class - A class of the output from 'SpaTopic'
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SpaTopic_inference() - 'SpaTopic': fast topic inference to identify tissue architecture in multiplexed images
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frex_topic() - Calculate FREX ranked words and values for a topic
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label_topics() - Label topics function
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lift_topic() - Calculate lift ranked words and values for a topic
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lung5 - Example input data for 'SpaTopic'
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print(<SpaTopic>) - Print method for SpaTopic objects
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prob_topic() - Calculate highest probability words and values for a topic
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score_topic() - Calculate score ranked words and values for a topic
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spatopic_message() - Format messages for SpaTopic package
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stratified_sampling_3D_via_2D() - Spatially stratified random sample points from a 3D image using 2D slicing.
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stratified_sampling_sf() - Spatially stratified random sample points from an image.