An Ecosystem for Exploring the Universe of Single-Cell Data
Overview
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.
Initial CRAN release
This is the first CRAN release of celliverse, an R toolkit for
clustering, marker discovery, cell-type annotation, and downstream
analysis of single-cell RNA-sequencing data.
Core single-cell analysis
- Added
clustoCell()for data-driven identification of major clusters and sub-clusters together with ranked positive and negative marker discovery. - Added the MarkoCell workflow for marker discovery from pre-defined clusters and user-selected cell subsets.
- Added functionality for cluster comparison, marker inspection, label transfer, integration with Seurat objects, and visualization of clustering and marker results.
Show all changes in 0.0.2Hide the rest of the changes in 0.0.2
Cell-type annotation
- Added the CelliVerse MarkerDB, distributed with the package as
markerDB, providing harmonized positive and negative cell-type marker information for human and mouse. - Added
typoClust()for annotation of ClustoCell/MarkoCell results using either the curated CelliVerse MarkerDB or LLM-assisted annotation. - Added
ceLLMarkup()for direct LLM-assisted annotation from marker panels, clustering results, or compatible marker tables. - Added
typoPrompt()for generating structured, model-independent cell-type annotation prompts that can be used with any preferred chatbot or LLM. - Added
saveTypoPrompt()for exporting TypoPrompt objects as plain-text or self-contained HTML documents.
CelliVerse Agent
- Added an optional LLM-powered CelliVerse Agent that provides a browser-based natural-language interface to CelliVerse workflows.
- Added
install_celliverse_agent()andrun_celliverse_agent()for Agent setup and launch. - Added support for common single-cell input formats, including R objects, delimited matrices, Matrix Market/10x inputs, zipped 10x triplets, and HDF5 inputs when the required optional dependency is available.
- Added support for both cloud-based model providers and local model backends such as Ollama and LM Studio.
Documentation and reproducibility
- Added a comprehensive package vignette covering clustering, marker discovery, annotation, visualization, TypoPrompt, and the CelliVerse Agent.
- Added expanded README documentation, installation guidance, interactive examples, and links to the browser-based ClustoCell demonstration.
- Added links to the dedicated CelliVerse-Project reproducibility repository containing manuscript analysis scripts and prepared MarkerDB resources.
- Computationally intensive and external-service-dependent examples are not executed during package checks; reproducible precomputed results are used where appropriate in the vignette.
From NEWS.md in the release
Install
Health
- OK13 OKNow
- OK5 OK2026-09-13
Documentation
The repository also keeps web-only articles.
- Help pages
- 27 (1 internal)includes a package overview page
- Examples that run
- 95%20 run in a plain check · 1 never run
- Exported functions with examples
- 91%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 4%
Downloads
Repository
- PRs merged (all time)
- not measured
- Median days to close, 50 most recently updated closed issues
- 0
- Median days to close, 50 most recently updated closed PRs
- not measured
Stars over time
Releases over time
8 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/asalavaty/celliverse on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows
GitHub Pages site last deployed 2026-09-14 · The repository has a site deploy workflow
pkgdown site last built 2026-09-14
Dependencies
Installing celliverse adds 136 packages (81 with compiled code, 127 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 1 more not on CRAN is not measured.
Code & Tests
Datasets
People & History
- 0.0.2Latestfirst seen 2026-09-12 · current release
- RR 4.6.0 released · 2026-04-24
Package metadata
- First seen
- 2026-09-12
- Total releases
- 1 / 1 yrs
- License
- GPL-3 OSI
- Minimum R
- ≥ 4.1.0
- Bundled data
- 1.3 MB / 3 files
- Download size
- 3.3 MB
Cite
Cite this package
Run in R for the authors' entry:
citation("celliverse")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1016/j.patter.2020.100052.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.