Package: geneXtendeR
Type: Package
Version: 1.0.0
Title: Optimal Gene Extensions From Histone Modification ChIP-seq Data
Description: geneXtendeR is designed to optimally annotate a histone
        modification ChIP-seq peak input file with functionally
        important genomic features (e.g., genes associated with peaks)
        based on optimization calculations.  geneXtendeR optimally
        extends the boundaries of every gene in a genome by some
        genomic distance (in DNA base pairs) for the purpose of
        flexibly incorporating cis-regulatory elements (CREs), such as
        enhancers and promoters, as well as downstream elements that
        are important to the function of the gene relative to an
        epigenetic histone modification ChIP-seq dataset. geneXtender
        computes optimal gene extensions tailored to the broadness of
        the specific epigenetic mark (e.g., H3K9me1, H3K27me3), as
        determined by a user-supplied ChIP-seq peak input file. As
        such, geneXtender maximizes the signal-to-noise ratio of
        locating genes closest to and directly under peaks. By
        performing a computational expansion of this nature, ChIP-seq
        reads that would initially not map strictly to a specific gene
        can now be optimally mapped to the regulatory regions of the
        gene, thereby implicating the gene as a potential candidate,
        and thereby making the ChIP-seq experiment more successful.
        Such an approach becomes particularly important when working
        with epigenetic histone modifications that have inherently
        broad peaks.
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: rtracklayer, R (>= 3.3.1)
Imports: data.table, dplyr, graphics, utils
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
License: GPL (>= 3)
LazyData: TRUE
biocViews: ChIPSeq, Genetics, Annotation, GenomeAnnotation,
        DifferentialPeakCalling, Coverage, PeakDetection, ChipOnChip,
        HistoneModification, DataImport
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-10-18 00:43:56 UTC; biocbuild
Author: Bohdan Khomtchouk [aut, cre]
Built: R 3.3.1; i386-w64-mingw32; 2016-10-18 02:34:41 UTC; windows
Archs: i386, x64
