An Ecosystem for Exploring the Universe of Single-Cell Data

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Documentation for package ‘celliverse’ version 0.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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