geneXtendeR

DOI: 10.18129/B9.bioc.geneXtendeR    

Optimized Functional Annotation Of ChIP-seq Data

Bioconductor version: Release (3.6)

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.

Author: Bohdan Khomtchouk [aut, cre]

Maintainer: Bohdan Khomtchouk <khomtchoukmed at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("geneXtendeR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("geneXtendeR")

 

PDF	R Script	geneXtendeR Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, GO, Genetics, GenomeAnnotation, HistoneModification, NaturalLanguageProcessing, PeakDetection, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.4 (R-3.3) (1.5 years)
License	GPL (>= 3)
Depends	GO.db, org.Rn.eg.db, rtracklayer, R (>= 3.3.1)
Imports	AnnotationDbi, data.table, dplyr, graphics, networkD3, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, RColorBrewer, SnowballC, tm, utils, wordcloud
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/Bohdan-Khomtchouk/geneXtendeR
BugReports	https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	geneXtendeR_1.4.0.tar.gz
Windows Binary	geneXtendeR_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	geneXtendeR_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/geneXtendeR
Package Short Url	http://bioconductor.org/packages/geneXtendeR/
Package Downloads Report	Download Stats