To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

biovizBase

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see biovizBase.

Basic graphic utilities for visualization of genomic data.

Bioconductor version: 3.1

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, Michael Lawrence, Dianne Cook

Maintainer: Tengfei Yin <yintengfei at gmail.com>

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

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 1.16.0
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License Artistic-2.0
Depends R (>= 2.10), methods
Imports grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors(>= 0.2.4), IRanges(>= 1.99.28), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.19), Biostrings(>= 2.33.11), Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.16), GenomicFeatures(>= 1.17.13), AnnotationDbi, VariantAnnotation(>= 1.11.4)
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer
SystemRequirements
Enhances
URL
Depends On Me CAFE, qrqc
Imports Me GenoView, ggbio, Gviz, Pviz, qrqc
Suggests Me derfinder, derfinderPlot, R3CPET, regionReport
Build Report

Package Archives

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

Package Source biovizBase_1.16.0.tar.gz
Windows Binary biovizBase_1.16.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) biovizBase_1.16.0.tgz
Mac OS X 10.9 (Mavericks) biovizBase_1.16.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/biovizBase/tree/release-3.1
Package Short Url http://bioconductor.org/packages/biovizBase/
Package Downloads Report Download Stats

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