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 (3.20)
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("biovizBase")
):
Installation
To install this package, start R (version "4.4") 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")
An Introduction to biovizBase | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Infrastructure, Preprocessing, Software, Visualization |
Version | 1.53.0 |
In Bioconductor since | BioC 2.9 (R-2.14) (13 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 |
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.
Source Package | biovizBase_1.53.0.tar.gz |
Windows Binary | biovizBase_1.53.0.zip (64-bit only) |
macOS Binary (x86_64) | biovizBase_1.53.0.tgz |
macOS Binary (arm64) | biovizBase_1.53.0.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 |