To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

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>

Citation (from within R, enter citation("geneXtendeR")):

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 year)
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

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