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methFuse  

Functional Segmentation of the Methylome
View on CRAN: Click here


Download and install methFuse package within the R console
Install from CRAN:
install.packages("methFuse")

Install from Github:
library("remotes")
install_github("cran/methFuse")

Install by package version:
library("remotes")
install_version("methFuse", "1.1.0")



Attach the package and use:
library("methFuse")
Maintained by
Susanna Holmström
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-03-04
Latest Update: 2026-03-04
Description:
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.
How to cite:
Susanna Holmström (2026). methFuse: Functional Segmentation of the Methylome. R package version 1.1.0, https://cran.r-project.org/web/packages/methFuse. Accessed 27 Oct. 2026.
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Complete documentation for methFuse
Functions, R codes and Examples using the methFuse R package
Full methFuse package functions and examples
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