To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("chromstaR")

In most cases, you don't need to download the package archive at all.

chromstaR

DOI: 10.18129/B9.bioc.chromstaR

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Bioconductor version: Release (3.5)

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:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("chromstaR")

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 ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, HistoneModification, MultipleComparison, Software
Version 1.2.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
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, ggbio
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package chromstaR_1.2.0.tar.gz
Windows Binary chromstaR_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) chromstaR_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/chromstaR
Package Short Url http://bioconductor.org/packages/chromstaR/
Package Downloads Report Download Stats

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