DOI: 10.18129/B9.bioc.geneXtendeR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see geneXtendeR.

Optimized Functional Annotation Of ChIP-seq Data

Bioconductor version: 3.13

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>

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biocViews Annotation, ChIPSeq, ChipOnChip, Coverage, DataImport, DifferentialPeakCalling, GO, Genetics, GenomeAnnotation, HistoneModification, NaturalLanguageProcessing, PeakDetection, Software, Visualization
Version 1.18.0
In Bioconductor since BioC 3.4 (R-3.3) (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,
Suggests knitr, rmarkdown, testthat,,,,,,,,,,, org.Sc.sgd.db,,, rtracklayer
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