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biovizBase

Basic graphic utilities for visualization of genomic data.


Bioconductor version: Release (3.18)

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>

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

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

Details

biocViews Infrastructure, Preprocessing, Software, Visualization
Version 1.50.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
System Requirements
URL
See More
Suggests BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit
Linking To
Enhances
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 Build Report

Package Archives

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

Source Package biovizBase_1.50.0.tar.gz
Windows Binary biovizBase_1.50.0.zip
macOS Binary (x86_64) biovizBase_1.50.0.tgz
macOS Binary (arm64) biovizBase_1.50.0.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