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Bioconductor - biovizBase (development version)

biovizBase

This is the development version of biovizBase; for the stable release version, see biovizBase.

Basic graphic utilities for visualization of genomic data.

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews Infrastructure, Preprocessing, Software, Visualization Version 1.57.1 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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), 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 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 Imports Me BubbleTree, ChIPexoQual, ggbio, Gviz, karyoploteR, Pviz, Rqc Suggests Me CINdex, Damsel, derfinderPlot, FRASER, NanoStringNCTools, OUTRIDER, R3CPET, regionReport, shiny.gosling, StructuralVariantAnnotation, Signac Links To Me Build Report Build Report Package Archives

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

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