chromstaR

DOI: 10.18129/B9.bioc.chromstaR    

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 (3.8)

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>

Citation (from within R, enter citation("chromstaR")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("chromstaR", version = "devel")

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, MultipleComparison, PeakDetection, Sequencing, Software
Version 1.7.3
In Bioconductor since BioC 3.4 (R-3.3) (2 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_1.7.3.tar.gz
Windows Binary chromstaR_1.7.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) chromstaR_1.7.3.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

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