Functional Segmentation of the Methylome R package methFuse version 1.1.0 Implements FUSE (Functional Segmentation of DNA methylation data), a data-driven method for identifying spatially coherent DNA methylation segments from whole-genome bisulfite sequencing (WGBS) count data. The method performs hierarchical clustering of CpG sites based on methylated and unmethylated read counts across multiple samples and determines the optimal number of segments using an information criterion (AIC or BIC). Resulting segments represent regions with homogeneous methylation profiles across the input cohort while allowing sample-specific methylation levels. The package provides functions for clustering, model selection, tree cutting, segment-level summarization, and visualization. Input can be supplied as count matrices or extracted directly from 'BSseq' and 'methrix' objects. Software Imports: stats, methods Suggests: bsseq, methrix, beachmat, GenomicRanges, SummarizedExperiment, DelayedArray, testthat (>= 3.0.0), knitr, rmarkdown, graphics Susanna Holmström <susanna.k.holmstrom@helsinki.fi> Comprehensive R Archive Network (CRAN) Susanna Holmström [aut, cre] (ORCID: <https://orcid.org/0009-0005-7542-5913>), Antti Hakkinen [ctb, cph] MIT + file LICENSE (https://CRAN.R-project.org/package=methFuse/LICENSE) 2026-03-04 application/tgz https://CRAN.R-project.org/package=methFuse doi:10.32614/CRAN.package.methFuse