GenomicOZone
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GenomicOZone.
Delineate outstanding genomic zones of differential gene activity
Bioconductor version: 3.12
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 [aut], Mingzhou Song [aut, cre]
Maintainer: Mingzhou Song <joemsong at cs.nmsu.edu>
citation("GenomicOZone")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| GenomicOZone | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 | 1.4.1 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | readxl, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicOZone_1.4.1.tar.gz |
| Windows Binary | GenomicOZone_1.4.1.zip |
| macOS 10.13 (High Sierra) | GenomicOZone_1.4.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicOZone |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicOZone |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicOZone/ |
| Package Short Url | https://bioconductor.org/packages/GenomicOZone/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |