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celliverse

celliverse 0.0.2

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.

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() and run_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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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