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Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Bioconductor version: Release (3.19)

Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.

Author: Mahmoud Ahmed [aut, cre]

Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy at>

Citation (from within R, enter citation("segmenter")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Chromatin Segmentation Analysis Using segmenter HTML R Script
Reference Manual PDF


biocViews HistoneModification, Software
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1)
Imports ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData
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Suggests testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
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Follow Installation instructions to use this package in your R session.

Source Package segmenter_1.10.0.tar.gz
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macOS Binary (x86_64) segmenter_1.10.0.tgz
macOS Binary (arm64) segmenter_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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