ggbio

Visualization tools for genomic data.

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("ggbio")

Documentation

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

Details

biocViews Infrastructure, Software, Visualization
Version 1.13.0
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends methods, BiocGenerics, ggplot2 (>= 0.9.3)
Imports grid, grDevices, graphics, stats, utils, biovizBase(>= 1.11.11), reshape2, gtable, Biobase, IRanges(>= 1.21.19), GenomicRanges(>= 1.13.3), GenomicFeatures, Rsamtools(>= 1.13.1), GenomicAlignments, BSgenome, gridExtra, scales, VariantAnnotation, Hmisc, rtracklayer, Biostrings, proto
Suggests vsn, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle
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 Downloads

Package Source ggbio_1.13.0.tar.gz
Windows Binary ggbio_1.13.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ggbio_1.13.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center