This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see GenomicOZone.
Bioconductor version: 3.10
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")
):
To install this package, start R (version "3.6") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomicOZone")
HTML | R Script | GenomicOZone |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, BiomedicalInformatics, CellBiology, Clustering, Coverage, DifferentialExpression, DifferentialMethylation, FunctionalGenomics, FunctionalPrediction, GeneExpression, GeneRegulation, Genetics, GenomicVariation, RNASeq, Regression, Sequencing, Software, StructuralVariation, SystemsBiology, Transcription, Transcriptomics, Visualization |
Version | 1.0.0 |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | GenomicOZone_1.0.0.tar.gz |
Windows Binary | GenomicOZone_1.0.0.zip |
Mac OS X 10.11 (El Capitan) | GenomicOZone_1.0.0.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 |
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