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DESCRIPTION
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DESCRIPTION
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Package: geneXtendeR
Type: Package
Version: 1.7.11
Title: Optimized Functional Annotation Of ChIP-seq Data
Description: 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.
Authors@R: c(
person("Bohdan", "Khomtchouk", email = "[email protected]", role = c("aut", "cre")),
person("William", "Koehler", email = "[email protected]", role = c("aut"))
)
Maintainer: Bohdan Khomtchouk <[email protected]>
URL: https://github.com/Bohdan-Khomtchouk/geneXtendeR
BugReports: https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues
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
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
VignetteBuilder: knitr
License: GPL (>= 3)
LazyData: TRUE
biocViews: ChIPSeq, Genetics, Annotation, GenomeAnnotation,
DifferentialPeakCalling, Coverage, PeakDetection, ChipOnChip,
HistoneModification, DataImport, NaturalLanguageProcessing, Visualization, GO, Software
RoxygenNote: 6.1.0
NeedsCompilation: yes
Encoding: UTF-8