biovizBase

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see biovizBase.

Basic graphic utilities for visualization of genomic data.

Bioconductor version: 3.10

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>

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

Installation

To install this package, start R (version "3.6") 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 1.34.1

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

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, RNAmodR, Rqc

Suggests Me CINdex, derfinder, derfinderPlot, R3CPET, regionReport, StructuralVariantAnnotation, TxRegInfra

Links To Me

Build Report Build Report

Package Archives

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

Source Package biovizBase_1.34.1.tar.gz

Windows Binary biovizBase_1.34.1.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) biovizBase_1.34.1.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

Old Source Packages for BioC 3.10 Source Archive