DOI: 10.18129/B9.bioc.GenomicOZone    

Delineate outstanding genomic zones of differential gene activity

Bioconductor version: Release (3.11)

The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. The method guarantees cluster optimality, linear runtime to sample size, and reproducibility. It enables new characterization of effects due to genome reorganization, structural variation, and epigenome alteration.

Author: Hua Zhong, Mingzhou Song

Maintainer: Hua Zhong<zh9118 at>, Mingzhou Song <joemsong at>

Citation (from within R, enter citation("GenomicOZone")):


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biocViews Annotation, BiomedicalInformatics, CellBiology, Clustering, Coverage, DifferentialExpression, DifferentialMethylation, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, Genetics, GenomicVariation, RNASeq, Regression, Sequencing, Software, StructuralVariation, SystemsBiology, Transcription, Transcriptomics, Visualization
Version 1.2.0
In Bioconductor since BioC 3.10 (R-3.6) (1 year)
License LGPL (>=3)
Depends R (>= 3.6), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2
Imports grDevices, stats, utils, plyr, gridExtra, sjstats, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack
Suggests readxl, GEOquery, knitr, rmarkdown
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