Package: celliverse 0.0.2.9000

celliverse: An Ecosystem for Exploring the Universe of Single-Cell Data

Contains functions for single-cell RNA sequencing data analysis. It provides core functionalities for clustering cells, identifying markers for predefined clusters, performing sub-clustering of major cell populations, and discovering markers within custom-selected subsets of cells. 'CelliVerse' also includes methods for analyzing cluster similarity and generating intuitive visualizations. Designed to be independent of library size and other sample- or cell-level confounding effects, 'CelliVerse' ensures reliable and interpretable results across a wide range of datasets. Fred Viole and David Nawrocki (2013, ISBN:1490523995). Csardi G, Nepusz T (2006). "The 'igraph' software package for complex network research." InterJournal, Complex Systems, 1695. Adopted algorithms and sources are referenced in function document.

Authors:Adrian Salavaty [aut, cre]

# Install 'celliverse' in R:

install.packages('celliverse', repos = c('https://asalavaty.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/asalavaty/celliverse/issues

Pkgdown/docs site:https://asalavaty.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

markerDB - Cell-type marker database
markerDictionary - Marker gene dictionary
tissueCondition_types - Tissue and condition reference catalog

On CRAN:

cpp

5.43 score 3 stars 6 scripts 974 downloads 23 exports 156 dependencies

Last updated from:ff3327b089. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	231
linux-devel-x86_64	OK	271
source / vignettes	OK	257
linux-release-arm64	OK	207
linux-release-x86_64	OK	307
macos-release-arm64	OK	204
macos-release-x86_64	OK	476
macos-oldrel-arm64	OK	159
macos-oldrel-x86_64	OK	352
windows-devel-arm64	OK	329
windows-devel-x86_64	OK	273
windows-release-arm64	OK	309
windows-release-x86_64	OK	221
windows-oldrel-x86_64	OK	235
wasm-release	OK	178

Exports:addClustoData addTypoData ceLLMarkup clustoCell clustoCell_TransferLabel ewcsr.sparse featureInspect getDatasetMarkers gini.ewcsr.fs gini.rank.fs install_celliverse_agent jaccard.sparse markerPurity markoCell markoClust markoClustVis mutual.rank run_celliverse_agent saveTypoPrompt signatureDotHeatmap typoClust typoClustVis typoPrompt

Dependencies:abind askpass base64enc BH Biobase BiocGenerics bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics GenomicRanges ggnewscale ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppThread RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject shiny sitmo sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zoo

Introduction to CelliVerse

Rendered fromIntroduction-to-CelliVerse.html.asisusingR.rsp::asis

Last update: 2026-08-18
Started: 2026-08-18

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

Package: celliverse 0.0.2.9000

celliverse: An Ecosystem for Exploring the Universe of Single-Cell Data

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