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DOI: 10.18129/B9.bioc.geneXtendeR    

Optimal Gene Extensions From Histone Modification ChIP-seq Data

Bioconductor version: Release (3.5)

geneXtendeR is designed to optimally annotate a histone modification ChIP-seq peak input file with functionally important genomic features (e.g., genes associated with peaks) based on optimization calculations. geneXtendeR optimally extends the boundaries of every gene in a genome by some genomic distance (in DNA base pairs) for the purpose of flexibly incorporating cis-regulatory elements (CREs), such as enhancers and promoters, as well as downstream elements that are important to the function of the gene relative to an epigenetic histone modification ChIP-seq dataset. geneXtender computes optimal gene extensions tailored to the broadness of the specific epigenetic mark (e.g., H3K9me1, H3K27me3), as determined by a user-supplied ChIP-seq peak input file. As such, geneXtender maximizes the signal-to-noise ratio of locating genes closest to and directly under peaks. By performing a computational expansion of this nature, ChIP-seq reads that would initially not map strictly to a specific gene can now be optimally mapped to the regulatory regions of the gene, thereby implicating the gene as a potential candidate, and thereby making the ChIP-seq experiment more successful. Such an approach becomes particularly important when working with epigenetic histone modifications that have inherently broad peaks.

Author: Bohdan Khomtchouk [aut, cre]

Maintainer: Bohdan Khomtchouk <khomtchoukmed at>

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biocViews Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, Genetics, GenomeAnnotation, HistoneModification, PeakDetection, Software
Version 1.2.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License GPL (>= 3)
Depends rtracklayer, R (>= 3.3.1)
Imports data.table, dplyr, graphics, utils
Suggests BiocStyle, knitr, rmarkdown
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