geneXtendeR

DOI: 10.18129/B9.bioc.geneXtendeR  

Optimized Functional Annotation Of ChIP-seq Data

Bioconductor version: Release (3.16)

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.

Author: Bohdan Khomtchouk [aut, cre], William Koehler [aut]

Maintainer: Bohdan Khomtchouk <khomtchoukmed at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

PDF		geneXtendeR.pdf
PDF		Reference Manual

Details

biocViews	Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, GO, Genetics, GenomeAnnotation, HistoneModification, NaturalLanguageProcessing, PeakDetection, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	GPL (>= 3)
Depends	rtracklayer, GO.db, R (>= 3.5.0)
Imports	data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db
LinkingTo
Suggests	knitr, rmarkdown, testthat, 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.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer
SystemRequirements
Enhances
URL	https://github.com/Bohdan-Khomtchouk/geneXtendeR
BugReports	https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	geneXtendeR_1.24.0.tar.gz
Windows Binary	geneXtendeR_1.24.0.zip
macOS Binary (x86_64)	geneXtendeR_1.24.0.tgz
macOS Binary (arm64)	geneXtendeR_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/geneXtendeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/geneXtendeR
Bioc Package Browser	https://code.bioconductor.org/browse/geneXtendeR/
Package Short Url	https://bioconductor.org/packages/geneXtendeR/
Package Downloads Report	Download Stats