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: 1.24.0
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: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:53:39 UTC
RemoteUrl: https://github.com/bioc/GenomicOZone
RemoteRef: RELEASE_3_22
RemoteSha: 0fee9199e942478816a23bf0403ae0c48603cc07
Packaged: 2025-11-11 19:19:00 UTC; root
Built: R 4.5.2; ; 2025-11-11 19:24:07 UTC; windows
