geneXtendeR
Optimized Functional Annotation Of ChIP-seq Data
Bioconductor version: Release (3.20)
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("geneXtendeR")):
Installation
To install this package, start R (version "4.4") 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.pdf | |
| Reference Manual |
Details
| biocViews | Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, GO, Genetics, GenomeAnnotation, HistoneModification, NaturalLanguageProcessing, PeakDetection, Software, Visualization |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | geneXtendeR_1.32.0.tar.gz |
| Windows Binary (x86_64) | geneXtendeR_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | geneXtendeR_1.32.0.tgz |
| macOS Binary (arm64) | geneXtendeR_1.32.0.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 |