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

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.

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

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/annotate.r R/barChart.r R/distinct.r R/linePlot.r R/peak_input_docs.r R/peaksInput.r R/rat.r
README
README.md
build
build/vignette.rds
data
data/datalist
data/rat.rda
data/samplepeaksinput.rda
inst
inst/CITATION
inst/doc
inst/doc/geneXtendeR.R
inst/doc/geneXtendeR.Rnw
inst/doc/geneXtendeR.pdf
inst/extdata
inst/extdata/somepeaksfile.txt
man
man/annotate.Rd man/barChart.Rd man/distinct.Rd man/linePlot.Rd man/peaksInput.Rd man/rat.Rd man/samplepeaksinput.Rd
src
src/annotate.c
src/extract_number.c
src/extract_peaks.c
vignettes
vignettes/figures
vignettes/figures/geneXtendeRlogo.png
vignettes/figures/workflow.pdf
vignettes/geneXtendeR.Rnw
vignettes/somepeaksfile.txt

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