# methFuse 1.1.0 (2026-02-19)

## New features
- Renamed package to methFuse to avoid name conflict in CRAN

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# fuseR 1.1.0 (2026-02-06)

## 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

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# fuseR 1.0.0 (2025-12-15)

## 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()`.

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# fuseR 0.0.0.9000 (2025-11-20)

## 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.


