Package: methFuse 1.1.0

Susanna Holmström

methFuse: Functional Segmentation of the Methylome

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:Susanna Holmström [aut, cre], Antti Hakkinen [ctb, cph]

methFuse_1.1.0.tar.gz
methFuse_1.1.0.tar.gz(r-4.7-arm64)methFuse_1.1.0.tar.gz(r-4.7-x86_64)methFuse_1.1.0.tar.gz(r-4.6-arm64)methFuse_1.1.0.tar.gz(r-4.6-x86_64)
methFuse_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
methFuse/json (API)
NEWS

# Install 'methFuse' in R:
install.packages('methFuse', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/holmsusa/methfuse/issues

Pkgdown/docs site:https://holmsusa.github.io

Uses libs:
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

openmp

2.70 score 3 scripts 463 downloads 5 exports 0 dependencies

Last updated from:36ab1c58ae. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK227
linux-devel-x86_64OK308
source / vignettesOK239
linux-release-arm64OK195
linux-release-x86_64OK205
wasm-releaseOK141

Exports:fuse.clusterfuse.cut.treefuse.segmentfuse.summarynumber.of.clusters

Dependencies:

Example workflow using FUSE

Susanna Holmstrom

Rendered fromexample.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-03-04
Started: 2026-03-04

Readme and manuals

Help Manual

Help pageTopics
Perform Hierarchical Clustering on Methylation Datafuse.cluster fuse.cluster.BSseq fuse.cluster.default fuse.cluster.methrix
Cut Hierarchical Clustering Tree into Clustersfuse.cut.tree
Full FUSE segmentation pipelinefuse.segment fuse.segment.BSseq fuse.segment.default fuse.segment.methrix
Summarize FUSE Segmentation Resultsfuse.summary
Find Optimal Number of Clustersnumber.of.clusters
Plot method for FUSE segmentation resultsplot.fuse_summary