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Changelog

Source: NEWS.md

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.