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segmenter

Perform Chromatin Segmentation Analysis in R by Calling ChromHMM


Bioconductor version: Release (3.18)

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 students.kasralainy.edu.eg>

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

Installation

To install this package, start R (version "4.3") 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.

Documentation

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

browseVignettes("segmenter")
Chromatin Segmentation Analysis Using segmenter HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews HistoneModification, Software
Version 1.8.0
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
System Requirements
URL
Bug Reports https://github.com/MahShaaban/segmenter/issues
See More
Suggests testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package segmenter_1.8.0.tar.gz
Windows Binary segmenter_1.8.0.zip
macOS Binary (x86_64) segmenter_1.8.0.tgz
macOS Binary (arm64) segmenter_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/segmenter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/segmenter
Bioc Package Browser https://code.bioconductor.org/browse/segmenter/
Package Short Url https://bioconductor.org/packages/segmenter/
Package Downloads Report Download Stats