GenomicOZone

DOI: 10.18129/B9.bioc.GenomicOZone    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GenomicOZone.

Delineate outstanding genomic zones of differential gene activity

Bioconductor version: 3.13

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.

Author: Hua Zhong, Mingzhou Song

Maintainer: Hua Zhong<zh9118 at gmail.com>, Mingzhou Song <joemsong at cs.nmsu.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

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, CopyNumberVariation, Coverage, DifferentialExpression, DifferentialMethylation, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, Genetics, GenomicVariation, RNASeq, Regression, Sequencing, Software, StructuralVariation, SystemsBiology, Transcription, Transcriptomics, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	LGPL (>=3)
Depends	R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2
Imports	grDevices, stats, utils, plyr, gridExtra, lsr, 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_1.6.0.tar.gz
Windows Binary	GenomicOZone_1.6.0.zip
macOS 10.13 (High Sierra)	GenomicOZone_1.6.0.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/
Package Downloads Report	Download Stats