biovizBase
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see biovizBase.
Basic graphic utilities for visualization of genomic data.
Bioconductor version: 3.9
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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Preprocessing, Software, Visualization |
| Version | 1.32.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), methods |
| Imports | grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors(>= 0.9.25), 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, 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_1.32.0.tar.gz |
| Windows Binary | biovizBase_1.32.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | biovizBase_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/biovizBase |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |