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 (2.14)

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 1.12.8
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends methods, BiocGenerics, ggplot2 (>= 1.0.0)
Imports grid, grDevices, graphics, stats, utils, biovizBase(>= 1.12.1), reshape2, gtable, Biobase, IRanges(>= 1.21.19), GenomicRanges(>= 1.13.3), GenomicFeatures, Rsamtools(>= 1.13.1), GenomicAlignments, BSgenome, gridExtra, scales, VariantAnnotation, Hmisc, rtracklayer, Biostrings
Suggests vsn, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, Homo.sapiens
System Requirements
URL http://tengfei.github.com/ggbio/
Depends On Me CAFE, intansv
Imports Me Rariant, ReportingTools, SomaticSignatures
Suggests Me beadarray, gwascat, interactiveDisplay, SomaticCancerAlterations

Package Archives

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

Package Source ggbio_1.12.8.tar.gz
Windows Binary ggbio_1.12.8.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ggbio_1.12.8.tgz
Mac OS X 10.9 (Mavericks) ggbio_1.12.8.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

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