chromstaR

DOI: 10.18129/B9.bioc.chromstaR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see chromstaR.

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	The chromstaR user's guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, HistoneModification, ImmunoOncology, MultipleComparison, PeakDetection, Sequencing, Software
Version	1.8.1
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 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
LinkingTo
Suggests	knitr, BiocStyle, testthat, biomaRt
SystemRequirements
Enhances
URL	https://github.com/ataudt/chromstaR
BugReports	https://github.com/ataudt/chromstaR/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	chromstaR_1.8.1.tar.gz
Windows Binary	chromstaR_1.8.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	chromstaR_1.8.1.tgz
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	http://bioconductor.org/packages/chromstaR/
Package Downloads Report	Download Stats