Package: geneXtendeR
Type: Package
Version: 1.6.0
Title: Optimized Functional Annotation Of ChIP-seq Data
Description: 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.
Authors@R: person("Bohdan", "Khomtchouk", email = "khomtchoukmed@gmail.com", role = c("aut", "cre"))
Maintainer: Bohdan Khomtchouk <khomtchoukmed@gmail.com>
URL: https://github.com/Bohdan-Khomtchouk/geneXtendeR
BugReports: https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues
Depends: GO.db, org.Rn.eg.db, rtracklayer, R (>= 3.3.1)
Imports: AnnotationDbi, data.table, dplyr, graphics, networkD3,
        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.Mmu.eg.db, org.Pt.eg.db, org.Sc.sgd.db,
        org.Ss.eg.db, org.Xl.eg.db, RColorBrewer, SnowballC, tm, utils,
        wordcloud
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
License: GPL (>= 3)
LazyData: TRUE
biocViews: ChIPSeq, Genetics, Annotation, GenomeAnnotation,
        DifferentialPeakCalling, Coverage, PeakDetection, ChipOnChip,
        HistoneModification, DataImport, NaturalLanguageProcessing,
        Visualization, GO, Software
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-05-01 03:50:05 UTC; biocbuild
Author: Bohdan Khomtchouk [aut, cre]
Built: R 3.5.0; i386-w64-mingw32; 2018-05-01 12:05:29 UTC; windows
Archs: i386, x64
