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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "methFuse" in publications use:'
type: software
license: MIT
title: 'methFuse: Functional Segmentation of the Methylome'
version: 1.1.0
doi: 10.32614/CRAN.package.methFuse
abstract: 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.
authors:
- family-names: Holmström
  given-names: Susanna
  email: susanna.k.holmstrom@helsinki.fi
  orcid: https://orcid.org/0009-0005-7542-5913
repository: https://holmsusa.r-universe.dev
commit: 3d9df163da82120f7fcf3affe77a68844b3f34b5
url: https://holmsusa.github.io/methFuse/
date-released: '2026-02-27'
contact:
- family-names: Holmström
  given-names: Susanna
  email: susanna.k.holmstrom@helsinki.fi
  orcid: https://orcid.org/0009-0005-7542-5913