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geneXtendeR

This is the development version of geneXtendeR; for the stable release version, see geneXtendeR.

Optimized Functional Annotation Of ChIP-seq Data


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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.pdf PDF
Reference Manual PDF

Details

biocViews Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, GO, Genetics, GenomeAnnotation, HistoneModification, NaturalLanguageProcessing, PeakDetection, Software, Visualization
Version 1.29.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements
URL https://github.com/Bohdan-Khomtchouk/geneXtendeR
Bug Reports https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues
See More
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
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Package Archives

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

Source Package geneXtendeR_1.29.0.tar.gz
Windows Binary geneXtendeR_1.29.0.zip (64-bit only)
macOS Binary (x86_64) geneXtendeR_1.29.0.tgz
macOS Binary (arm64) geneXtendeR_1.29.0.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/
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