segmenter
Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
Bioconductor version: 3.24 · Package version: 1.19.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("segmenter")Details
| Maintainer | Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg> |
| Author | Mahmoud Ahmed [aut, cre] (ORCID: <https://orcid.org/0000-0002-4377-6541>) |
| License | GPL-3 |
| Bug Reports | https://github.com/MahShaaban/segmenter/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | HistoneModification, Software |
| Package Short Url | https://bioconductor.org/packages/segmenter/ |
Citation
From within R, enter citation("segmenter"):
Mahmoud Ahmed. segmenter: Perform Chromatin Segmentation Analysis in R by Calling ChromHMM. doi:10.18129/B9.bioc.segmenter, R package version 1.19.0, https://bioconductor.org/packages/segmenter.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | segmenter_1.19.0.tar.gz |
| Windows binary (x86_64) | segmenter_1.19.0.zip |
| macOS binary (arm64) | segmenter_1.19.0.tgz |
| macOS binary (x86_64) | segmenter_1.19.0.tgz |
Dependencies
Depends: R (>= 4.1)
Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData
Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz