To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

ggbio

 

   

This is the development version of ggbio; for the stable release version, see ggbio.

Visualization tools for genomic data.

Bioconductor version: Development (3.4)

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>

Citation (from within R, enter citation("ggbio")):

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

Details

biocViews Infrastructure, Software, Visualization
Version 1.21.4
In Bioconductor since BioC 2.9 (R-2.14) (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(>= 1.19.1), Biobase, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.21.10), SummarizedExperiment, Biostrings, Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.16), BSgenome, VariantAnnotation(>= 1.11.4), rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.17.13), OrganismDbi, GGally, ensembldb(>= 1.3.8), AnnotationDbi
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
SystemRequirements
Enhances
URL http://tengfei.github.com/ggbio/
BugReports https://github.com/tengfei/ggbio/issues
Depends On Me CAFE, coMET, intansv
Imports Me derfinderPlot, FourCSeq, gwascat, R3CPET, Rariant, ReportingTools, RiboProfiling, SomaticSignatures
Suggests Me beadarray, chromstaR, GoogleGenomics, gQTLstats, interactiveDisplay, regionReport, RnBeads, Single.mTEC.Transcriptomes, SomaticCancerAlterations
Build Report  

Package Archives

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

Package Source ggbio_1.21.4.tar.gz
Windows Binary ggbio_1.21.4.zip
Mac OS X 10.9 (Mavericks) ggbio_1.21.4.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ggbio
Package Short Url http://bioconductor.org/packages/ggbio/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: