geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

Getting started

Package details

AuthorBohdan Khomtchouk [aut, cre], William Koehler [aut]
Bioconductor views Annotation ChIPSeq ChipOnChip Coverage DataImport DifferentialPeakCalling GO Genetics GenomeAnnotation HistoneModification NaturalLanguageProcessing PeakDetection Software Visualization
MaintainerBohdan Khomtchouk <[email protected]>
LicenseGPL (>= 3)
Version1.8.0
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 Nov. 1, 2018, 3:34 a.m.