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]|
|Bioconductor views||Annotation ChIPSeq ChipOnChip Coverage DataImport DifferentialPeakCalling GO Genetics GenomeAnnotation HistoneModification NaturalLanguageProcessing PeakDetection Software Visualization|
|Maintainer||Bohdan Khomtchouk <[email protected]>|
|License||GPL (>= 3)|
|Package repository||View on Bioconductor|
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