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

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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]
Date of publication
None
Maintainer
Bohdan Khomtchouk <khomtchoukmed@gmail.com>
License
GPL (>= 3)
Version
1.0.0
URLs

View on Bioconductor

Man pages

annotate
Annotate peaks file.
barChart
Produces bar charts.
distinct
Finds unique genes under peaks.
linePlot
Produces line plots.
peaksInput
Preprocesses a peaks input file.
rat
Gene transfer format (GTF) file for rat...
samplepeaksinput
Sample peaks list to be used as input to geneXtendeR

Files in this package

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