geneXtendeR

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see geneXtendeR.

Optimized Functional Annotation Of ChIP-seq Data

Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("geneXtendeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("geneXtendeR")

geneXtendeR Vignette	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, GO, Genetics, GenomeAnnotation, HistoneModification, NaturalLanguageProcessing, PeakDetection, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.4 (R-3.3) (7.5 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
System Requirements
URL	https://github.com/Bohdan-Khomtchouk/geneXtendeR
Bug Reports	https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues

Suggests	BiocStyle, knitr, rmarkdown
Linking To
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Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	geneXtendeR_1.6.0.tar.gz
Windows Binary	geneXtendeR_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	geneXtendeR_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/geneXtendeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/geneXtendeR
Package Short Url	https://bioconductor.org/packages/geneXtendeR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.7	Source Archive