segmenter

This is the development version of segmenter; for the stable release version, see segmenter.

Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Bioconductor version: Development (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: )

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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	HistoneModification, Software
Version	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 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

Suggests	testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	segmenter_1.13.0.tar.gz
Windows Binary (x86_64)	segmenter_1.13.0.zip (64-bit only)
macOS Binary (x86_64)	segmenter_1.13.0.tgz
macOS Binary (arm64)
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