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("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 | ||
| NEWS | Text |
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 |
See More
| 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) | segmenter_1.13.0.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 |