biovizBase

DOI: 10.18129/B9.bioc.biovizBase  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see biovizBase.

Basic graphic utilities for visualization of genomic data.

Bioconductor version: 3.17

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 <michafla at gene.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("biovizBase")

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("biovizBase")

 

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

Details

biocViews	Infrastructure, Preprocessing, Software, Visualization
Version	1.48.0
In Bioconductor since	BioC 2.9 (R-2.14) (12 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), methods
Imports	grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors(>= 0.23.19), 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), rlang
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, derfinderPlot, NanoStringNCTools, R3CPET, regionReport, StructuralVariantAnnotation
Links To Me
Build Report

Package Archives

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

Source Package	biovizBase_1.48.0.tar.gz
Windows Binary	biovizBase_1.48.0.zip (64-bit only)
macOS Binary (x86_64)	biovizBase_1.48.0.tgz
macOS Binary (arm64)	biovizBase_1.48.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biovizBase
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biovizBase
Bioc Package Browser	https://code.bioconductor.org/browse/biovizBase/
Package Short Url	https://bioconductor.org/packages/biovizBase/
Package Downloads Report	Download Stats