chromstaR
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see chromstaR.
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Bioconductor version: 3.9
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 "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chromstaR")
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("chromstaR")| The chromstaR user's guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, HistoneModification, ImmunoOncology, MultipleComparison, PeakDetection, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3), GenomicRanges, ggplot2, chromstaRData |
| Imports | methods, utils, grDevices, graphics, stats, foreach, doParallel, 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 | chromstaR_1.10.0.tar.gz |
| Windows Binary | chromstaR_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | chromstaR_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/chromstaR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/chromstaR |
| Bioc Package Browser | https://code.bioconductor.org/browse/chromstaR/ |
| Package Short Url | https://bioconductor.org/packages/chromstaR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |