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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biovizBase")
In most cases, you don't need to download the package archive at all.
biovizBase
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see biovizBase.
Basic graphic utilities for visualization of genomic data.
Bioconductor version: 3.4
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biovizBase")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("biovizBase")
| R Script | An Introduction to biovizBase | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Infrastructure, Preprocessing, Software, Visualization |
| Version | 1.22.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (5.5 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(>= 1.3.8) |
| LinkingTo | |
| Suggests | BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | CAFE, qrqc |
| Imports Me | BubbleTree, ggbio, Gviz, Pviz, qrqc, Rqc |
| Suggests Me | CINdex, derfinder, derfinderPlot, R3CPET, regionReport |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | biovizBase_1.22.0.tar.gz |
| Windows Binary | biovizBase_1.22.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | biovizBase_1.22.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/biovizBase/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/biovizBase/ |
| Package Downloads Report | Download Stats |
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