geneXtendeR: Optimal Gene Extensions From Histone Modification ChIP-seq Data
Version 1.2.0

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.

Package details

AuthorBohdan Khomtchouk [aut, cre]
Bioconductor views Annotation ChIPSeq ChipOnChip Coverage DataImport DifferentialPeakCalling Genetics GenomeAnnotation HistoneModification PeakDetection
MaintainerBohdan Khomtchouk <khomtchoukmed@gmail.com>
LicenseGPL (>= 3)
Version1.2.0
URL https://github.com/Bohdan-Khomtchouk/geneXtendeR
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("geneXtendeR")

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geneXtendeR documentation built on May 31, 2017, 3:29 p.m.