Package: GenomicOZone
Type: Package
Title: Delineate outstanding genomic zones of differential gene
        activity
biocViews: Software, GeneExpression, Transcription,
        DifferentialExpression, FunctionalPrediction, GeneRegulation,
        BiomedicalInformatics, CellBiology, FunctionalGenomics,
        Genetics, SystemsBiology, Transcriptomics, Clustering,
        Regression, RNASeq, Annotation, Visualization, Sequencing,
        Coverage, DifferentialMethylation, GenomicVariation,
        StructuralVariation, CopyNumberVariation
Version: 1.27.0
Date: 2025-07-22
Author: Hua Zhong, Mingzhou Song
Maintainer: Hua Zhong<zh9118@gmail.com>, Mingzhou Song
 <joemsong@cs.nmsu.edu>
Description: The package clusters gene activity along chromosome into
        zones, detects differential zones as outstanding, and
        visualizes maps of outstanding zones across the genome. It
        enables characterization of effects on multiple genes within
        adaptive genomic neighborhoods, which could arise from genome
        reorganization, structural variation, or epigenome alteration.
        It guarantees cluster optimality, linear runtime to sample
        size, and reproducibility. One can apply it on genome-wide
        activity measurements such as copy number, transcriptomic,
        proteomic, and methylation data.
License: LGPL (>=3)
Encoding: UTF-8
NeedsCompilation: no
Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges,
        biomaRt, ggplot2
Suggests: readxl, GEOquery, knitr, rmarkdown
Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel,
        ggbio, S4Vectors, IRanges, Seqinfo, Rdpack
RdMacros: Rdpack
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:50:43 UTC
RemoteUrl: https://github.com/bioc/GenomicOZone
RemoteRef: HEAD
RemoteSha: 4bb542aa21f7badbcbad7904813fe44666d1d74e
Packaged: 2026-07-13 05:56:07 UTC; root