chromstaR
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is the development version of chromstaR; for the stable release version, see chromstaR.
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Bioconductor version: Development (3.21)
This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.
Author: Aaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen
Maintainer: Aaron Taudt <aaron.taudt at gmail.com>
citation("chromstaR")):
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("chromstaR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ATACSeq, ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, HistoneModification, ImmunoOncology, MultipleComparison, PeakDetection, Sequencing, Software |
| Version | 1.33.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), GenomicRanges, ggplot2, chromstaRData |
| Imports | methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics(>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm |
| System Requirements | |
| URL | https://github.com/ataudt/chromstaR |
| Bug Reports | https://github.com/ataudt/chromstaR/issues |
See More
| Suggests | knitr, BiocStyle, testthat, biomaRt |
| 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 | |
| Windows Binary (x86_64) | chromstaR_1.33.1.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/chromstaR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/chromstaR |
| Package Short Url | https://bioconductor.org/packages/chromstaR/ |
| Package Downloads Report | Download Stats |