This is the released version of segmenter; for the devel version, see segmenter.
Perform Chromatin Segmentation Analysis in R by Calling ChromHMMBioconductor version: Release (3.21)
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] ORCID: 0000-0002-4377-6541
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy at students.kasralainy.edu.eg>
Citation (from within R, entercitation("segmenter")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("segmenter")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("segmenter")Follow Installation instructions to use this package in your R session.
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