Changes in version 0.0.2.9000                      

  - Update README. Package is on CRAN.

                 Changes in version 0.0.2 (2026-09-12)                  

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.