Bioconductor-mirror/geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data
Version 1.3.5

geneXtendeR optimizes the functional annotation of ChIP-seq peaks using fast iterative peak-coordinate/GTF alignment algorithms. 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 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

Bioconductor views Annotation ChIPSeq ChipOnChip Coverage DataImport DifferentialPeakCalling GO Genetics GenomeAnnotation HistoneModification NaturalLanguageProcessing PeakDetection Software Visualization
MaintainerBohdan Khomtchouk <[email protected]>
LicenseGPL (>= 3)
Version1.3.5
URL https://github.com/Bohdan-Khomtchouk/geneXtendeR
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("Bioconductor-mirror/geneXtendeR")
Bioconductor-mirror/geneXtendeR documentation built on Aug. 8, 2017, 5:48 a.m.