biovizBase

DOI: 10.18129/B9.bioc.biovizBase    

Basic graphic utilities for visualization of genomic data.

Bioconductor version: Release (3.6)

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

Author: Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]

Maintainer: Michael Lawrence <lawrence.michael at gene.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biovizBase")

Documentation

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

browseVignettes("biovizBase")

 

PDF	R Script	An Introduction to biovizBase
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Preprocessing, Software, Visualization
Version	1.26.0
In Bioconductor since	BioC 2.9 (R-2.14) (6.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods
Imports	grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors(>= 0.9.25), IRanges(>= 1.99.28), GenomeInfoDb(>= 1.5.14), GenomicRanges(>= 1.23.21), SummarizedExperiment, Biostrings(>= 2.33.11), Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.16), GenomicFeatures(>= 1.21.19), AnnotationDbi, VariantAnnotation(>= 1.11.4), ensembldb(>= 1.99.13), AnnotationFilter(>= 0.99.8)
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit
SystemRequirements
Enhances
URL
Depends On Me	CAFE, qrqc
Imports Me	BubbleTree, ChIPexoQual, ggbio, Gviz, karyoploteR, Pviz, qrqc, Rqc
Suggests Me	CINdex, derfinder, derfinderPlot, R3CPET, regionReport
Build Report

Package Archives

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

Source Package	biovizBase_1.26.0.tar.gz
Windows Binary	biovizBase_1.26.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	biovizBase_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biovizBase
Package Short Url	http://bioconductor.org/packages/biovizBase/
Package Downloads Report	Download Stats