To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ggbio")

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

ggbio

 

Visualization tools for genomic data.

Bioconductor version: Release (3.1)

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, Dianne Cook, Michael Lawrence

Maintainer: Tengfei Yin <yintengfei at gmail.com>

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

Installation

To install this package, start R and enter:

source("http://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 R Script Part 0: Introduction and quick start
PDF   Reference Manual
Text   NEWS

Details

biocViews Infrastructure, Software, Visualization
Version 1.16.1
In Bioconductor since BioC 2.9 (R-2.14) (3.5 years)
License Artistic-2.0
Depends methods, BiocGenerics, ggplot2 (>= 1.0.0)
Imports grid, grDevices, graphics, stats, utils, biovizBase(>= 1.13.8), reshape2, gtable, Biobase, S4Vectors(>= 0.2.3), IRanges(>= 1.99.28), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.40), Biostrings, Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.16), BSgenome, gridExtra, scales, VariantAnnotation(>= 1.11.4), Hmisc, rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.17.13), OrganismDbi, GGally
LinkingTo
Suggests vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat
SystemRequirements
Enhances
URL http://tengfei.github.com/ggbio/
BugReports https://github.com/tengfei/ggbio/issues
Depends On Me CAFE, intansv
Imports Me coMET, derfinderPlot, FourCSeq, GenoView, R3CPET, Rariant, regionReport, ReportingTools, SomaticSignatures
Suggests Me beadarray, GoogleGenomics, gQTLstats, gwascat, interactiveDisplay, RnBeads, SomaticCancerAlterations
Build Report  

Package Archives

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

Package Source ggbio_1.16.1.tar.gz
Windows Binary ggbio_1.16.1.zip
Mac OS X 10.6 (Snow Leopard) ggbio_1.16.1.tgz
Mac OS X 10.9 (Mavericks) ggbio_1.16.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ggbio/tree/release-3.1
Package Short Url http://bioconductor.org/packages/ggbio/
Package Downloads Report Download Stats

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