segmenter

DOI: 10.18129/B9.bioc.segmenter  

Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Chromatin Segmentation Analysis Using segmenter
PDF		Reference Manual
Text		NEWS

Details

biocViews	HistoneModification, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData
LinkingTo
Suggests	testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
SystemRequirements
Enhances
URL
BugReports	https://github.com/MahShaaban/segmenter/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	segmenter_1.4.0.tar.gz
Windows Binary	segmenter_1.4.0.zip
macOS Binary (x86_64)	segmenter_1.4.0.tgz
macOS Binary (arm64)	segmenter_1.4.0.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