biovizBase
This is the released version of biovizBase; for the devel version, see biovizBase.
Basic graphic utilities for visualization of genomic data.
Bioconductor version: Release (3.23)
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 <lawremi at gmail.com>
citation("biovizBase")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.60.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 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 | ChIPexoQual, ggbio, Gviz, karyoploteR, Pviz, Rqc |
| Suggests Me | 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_1.60.0.tar.gz |
| Windows Binary (x86_64) | biovizBase_1.60.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | biovizBase_1.60.0.tgz |
| macOS Binary (sonoma-arm64) | biovizBase_1.60.0.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 |