biovizBase

This is the released version of biovizBase; for the devel version, see biovizBase.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

Basic graphic utilities for visualization of genomic data.

Bioconductor version: Release (3.23)

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 <lawremi at gmail.com>

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

Tengfei Yin, Michael Lawrence, Dianne Cook. biovizBase: Basic graphic utilities for visualization of genomic data. doi:10.18129/B9.bioc.biovizBase, R package version 1.60.0, https://bioconductor.org/packages/biovizBase.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Preprocessing, Software, Visualization
Version	1.60.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 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), Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), AnnotationDbi, VariantAnnotation (>= 1.55.1), ensembldb (>= 2.33.1), AnnotationFilter (>= 0.99.8), rlang
System Requirements
URL

Suggests	BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit
Linking To
Enhances
Depends On Me	CAFE
Imports Me	BubbleTree, ChIPexoQual, ggbio, Gviz, karyoploteR, Pviz, Rqc
Suggests Me	Damsel, derfinderPlot, FRASER, NanoStringNCTools, OUTRIDER, R3CPET, regionReport, shiny.gosling, Signac, StructuralVariantAnnotation
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	biovizBase_1.60.0.tar.gz
Windows Binary (x86_64)	biovizBase_1.60.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	biovizBase_1.60.0.tgz
macOS Binary (sonoma-arm64)	biovizBase_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biovizBase
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biovizBase
Package Short Url	https://bioconductor.org/packages/biovizBase/
Package Downloads Report	Download Stats