Package index
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addClustoData() - Add ClustoCell cluster annotations to a Seurat or SingleCellExperiment object
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addTypoData() - Add TypoClust cell type annotations to a single-cell object
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ceLLMarkup() - LLM-based cell-type annotation of clusters or marker sets (ceLLMarkup)
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clustoCell() - Clustering and marker discovery for single-cell data using EWCSR-based similarity
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clustoCell_TransferLabel() - Transfer ClustoCell cluster labels to a full-resolution dataset
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ewcsr.sparse() - Compute expression-weighted centered scaled ranks (EWCSR)
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featureInspect() - Inspect the Membership of Features Across ClustoCell Results
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getDatasetMarkers() - Collect marker genes from a ClustoCell object
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gini.ewcsr.fs() - Feature selection using Gini coefficient on EWCSR-transformed data
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gini.rank.fs() - Feature selection using Gini coefficient on ranked expression data
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install_celliverse_agent() - Prepare this machine to run the CelliVerse agent
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jaccard.sparse() - Compute Jaccard similarity for sparse matrices
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markerDB - Cell-type marker database
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markerDictionary - Marker gene dictionary
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markerPurity() - Assess marker purity across clusters or cell subsets
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markoCell() - Rank markers for clusters, cell subsets, or individual cells
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markoClust() - Evaluate and refine cell clusters using marker ranking and graph partitioning
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markoClustVis() - Visualize cluster and cell-subset markers
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mutual.rank() - Compute mutual rank from a similarity matrix
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run_celliverse_agent() - Launch the CelliVerse agent (API + UI)
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saveTypoPrompt() - Save a TypoPrompt to a file
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signatureDotHeatmap() - Visualize per-signature marker expression across clusters
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tissueCondition_types - Tissue and condition reference catalog
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typoClust() - Cell type annotation of clusters, sub-clusters, or cell subsets
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typoClustVis() - Visualization of TypoClust cell-type annotations
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typoPrompt() - Generate an LLM-ready prompt for cell-type annotation