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: 1.23.1
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
git_url: https://git.bioconductor.org/packages/GenomicOZone
git_branch: devel
git_last_commit: fb1a6be
git_last_commit_date: 2025-07-22
Repository: Bioconductor 3.22
Date/Publication: 2025-07-23
Packaged: 2025-07-23 23:25:53 UTC; biocbuild
Built: R 4.5.1; ; 2025-07-24 13:13:17 UTC; windows
