GenomicOZone

DOI: 10.18129/B9.bioc.GenomicOZone    

This is the development version of GenomicOZone; for the stable release version, see GenomicOZone.

Delineate outstanding genomic zones of differential gene activity

Bioconductor version: Development (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 gmail.com>, Mingzhou Song <joemsong at cs.nmsu.edu>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GenomicOZone")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicOZone")

 

HTML R Script GenomicOZone
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, BiomedicalInformatics, CellBiology, Clustering, Coverage, DifferentialExpression, DifferentialMethylation, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, Genetics, GenomicVariation, RNASeq, Regression, Sequencing, Software, StructuralVariation, SystemsBiology, Transcription, Transcriptomics, Visualization
Version 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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
LinkingTo
Suggests readxl, GEOquery, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GenomicOZone_1.1.0.tar.gz
Windows Binary GenomicOZone_1.1.0.zip
Mac OS X 10.11 (El Capitan) GenomicOZone_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicOZone
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicOZone
Package Short Url https://bioconductor.org/packages/GenomicOZone/
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