Changes in version 1.1.0 (2026-03-04)                  

New features

  - Renamed package to methFuse to avoid name conflict in CRAN

New features

  - Added fuse.cluster() support for BSseq and methrix objects
  - Added fuse.segment() support for BSseq and methrix objects
  - Unified S3 API: fuse.cluster(K0, K1) and fuse.segment(K0, K1) now
    supported
  - fuse.cluster() now returns an hclust object

Improvements

  - Improved internal argument normalization for matrix inputs
  - Expanded test coverage for Bioconductor classes

Bug fixes

  - Fixed incorrect handling of positional K1 arguments in S3 methods
  - Fixed bug in plotting
  - Now works in Windows OS

                        Changes in version 1.0.0                        

New features

  - Added plot.fuse_summary() S3 method for visualization of FUSE
    segmentation results.
  - Segment plots now display:
      - Horizontal segment-level methylation estimates
      - Per-segment average beta values
      - Optional per-CpG methylation values overlaid as background
        points
  - Added support for flexible segment selection when plotting
    (segments_to_plot).

Improvements

  - Promoted package to first stable release (1.0.0).
  - Improved input validation and error handling across exported
    functions.
  - Improved S3 method registration and namespace imports.
  - Improved vignette robustness and reproducibility during package
    checks.
  - Updated documentation to reflect current plotting and summary
    capabilities.

Bug fixes

  - Fixed S3 dispatch issues affecting plot() during vignette building.
  - Fixed lazy-load and installation issues caused by partial rebuilds.
  - Fixed edge cases in beta computation when counts sum to zero.
  - Fixed the swapped TRUE/FALSE labels for coherent segments in
    fuse.summary().

                     Changes in version 0.0.0.9000                      

Initial development release

  - Implemented core FUSE pipeline:
      - fuse.cluster()
      - number.of.clusters()
      - fuse.cut.tree()
      - fuse.summary()
      - fuse.segment() (full pipeline wrapper)
  - Included basic example data files for testing.
  - Added introductory README and MIT license.
  - Added full example workflow as an R Markdown vignette (example.Rmd).
  - Enabled automatic pkgdown site deployment via GitHub Actions.