To install this package, start R and enter:

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

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

geneXtendeR

 

   

Optimal Gene Extensions From Histone Modification ChIP-seq Data

Bioconductor version: Release (3.4)

geneXtendeR is designed to optimally annotate a histone modification ChIP-seq peak input file with functionally important genomic features (e.g., genes associated with peaks) based on optimization calculations. geneXtendeR optimally extends the boundaries of every gene in a genome by some genomic distance (in DNA base pairs) for the purpose of flexibly incorporating cis-regulatory elements (CREs), such as enhancers and promoters, as well as downstream elements that are important to the function of the gene relative to an epigenetic histone modification ChIP-seq dataset. geneXtender computes optimal gene extensions tailored to the broadness of the specific epigenetic mark (e.g., H3K9me1, H3K27me3), as determined by a user-supplied ChIP-seq peak input file. As such, geneXtender maximizes the signal-to-noise ratio of locating genes closest to and directly under peaks. By performing a computational expansion of this nature, ChIP-seq reads that would initially not map strictly to a specific gene can now be optimally mapped to the regulatory regions of the gene, thereby implicating the gene as a potential candidate, and thereby making the ChIP-seq experiment more successful. Such an approach becomes particularly important when working with epigenetic histone modifications that have inherently broad peaks.

Author: Bohdan Khomtchouk [aut, cre]

Maintainer: Bohdan Khomtchouk <khomtchoukmed at gmail.com>

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("geneXtendeR")

 

PDF R Script geneXtendeR Vignette
PDF   Reference Manual
Text   README

Details

biocViews Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, Genetics, GenomeAnnotation, HistoneModification, PeakDetection, Software
Version 1.0.0
In Bioconductor since BioC 3.4 (R-3.3) (< 6 months)
License GPL (>= 3)
Depends rtracklayer, R (>= 3.3.1)
Imports data.table, dplyr, graphics, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/Bohdan-Khomtchouk/geneXtendeR
BugReports https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source geneXtendeR_1.0.0.tar.gz
Windows Binary geneXtendeR_1.0.0.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) geneXtendeR_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/geneXtendeR/tree/release-3.4
Package Short Url http://bioconductor.org/packages/geneXtendeR/
Package Downloads Report Download Stats

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