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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
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see chromstaR.
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Bioconductor version: 3.4
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")
| R Script | The chromstaR user's guide | |
| Reference Manual |
Details
| biocViews | ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, MultipleComparison, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 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 |
| 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.
| Package Source | chromstaR_1.0.0.tar.gz |
| Windows Binary | chromstaR_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | chromstaR_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/chromstaR/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/chromstaR/ |
| Package Downloads Report | Download Stats |
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