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: 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")
| R Script | Part 0: Introduction and quick start | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Infrastructure, Software, Visualization |
| Version | 1.12.10 |
| 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_1.12.10.tar.gz |
| Windows Binary | ggbio_1.12.10.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ggbio_1.12.10.tgz |
| Mac OS X 10.9 (Mavericks) | ggbio_1.12.10.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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