ggbio

DOI: 10.18129/B9.bioc.ggbio    

Visualization tools for genomic data

Bioconductor version: Release (3.6)

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Author: Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]

Maintainer: Michael Lawrence <lawrence.michael at gene.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ggbio")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ggbio")

 

PDF		Part 0: Introduction and quick start
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software, Visualization
Version	1.26.1
In Bioconductor since	BioC 2.9 (R-2.14) (6.5 years)
License	Artistic-2.0
Depends	methods, BiocGenerics, ggplot2 (>= 1.0.0)
Imports	grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase(>= 1.23.3), Biobase, S4Vectors(>= 0.13.13), IRanges(>= 2.11.16), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.16), BSgenome, VariantAnnotation(>= 1.11.4), rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.29.11), OrganismDbi, GGally, ensembldb(>= 1.99.13), AnnotationDbi, AnnotationFilter
LinkingTo
Suggests	vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex
SystemRequirements
Enhances
URL	http://tengfei.github.com/ggbio/
BugReports	https://github.com/tengfei/ggbio/issues
Depends On Me	CAFE, coMET, intansv
Imports Me	amplican, derfinderPlot, FourCSeq, gwascat, msgbsR, Pi, R3CPET, Rariant, ReportingTools, RiboProfiling, SomaticSignatures
Suggests Me	beadarray, chromstaR, ensembldb, GoogleGenomics, gQTLstats, interactiveDisplay, regionReport, RnBeads, Single.mTEC.Transcriptomes, SomaticCancerAlterations
Build Report

Package Archives

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

Source Package	ggbio_1.26.1.tar.gz
Windows Binary	ggbio_1.26.1.zip
Mac OS X 10.11 (El Capitan)	ggbio_1.26.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ggbio
Package Short Url	http://bioconductor.org/packages/ggbio/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive