DOI: 10.18129/B9.bioc.geneXtendeR    

Optimized Functional Annotation Of ChIP-seq Data

Bioconductor version: Release (3.6)

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]

Maintainer: Bohdan Khomtchouk <khomtchoukmed at>

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biocViews Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, GO, Genetics, GenomeAnnotation, HistoneModification, NaturalLanguageProcessing, PeakDetection, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
License GPL (>= 3)
Depends GO.db,, rtracklayer, R (>= 3.3.1)
Imports AnnotationDbi, data.table, dplyr, graphics, networkD3,,,,,,,,,,,, org.Sc.sgd.db,,, RColorBrewer, SnowballC, tm, utils, wordcloud
Suggests BiocStyle, knitr, rmarkdown
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