segmenter

DOI: 10.18129/B9.bioc.segmenter    

Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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
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Details

biocViews HistoneModification, Software
Version 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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_1.0.0.tar.gz
Windows Binary segmenter_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) segmenter_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/segmenter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/segmenter
Package Short Url https://bioconductor.org/packages/segmenter/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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