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DOI: 10.18129/B9.bioc.ggbio    

Visualization tools for genomic data

Bioconductor version: Release (3.5)

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>

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


biocViews Infrastructure, Software, Visualization
Version 1.24.1
In Bioconductor since BioC 2.9 (R-2.14) (6 years)
License Artistic-2.0
Depends methods, BiocGenerics, ggplot2 (>= 1.0.0)
Imports grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase(>= 1.23.3), Biobase, S4Vectors(>= 0.13.13), 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(>= 1.99.13), AnnotationDbi, AnnotationFilter
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
Depends On Me CAFE, coMET, intansv
Imports Me derfinderPlot, FourCSeq, gwascat, msgbsR, Pi, R3CPET, Rariant, ReportingTools, RiboProfiling, SomaticSignatures
Suggests Me beadarray, chromstaR, ensembldb, GoogleGenomics, gQTLstats, interactiveDisplay, regionReport, RnBeads, Single.mTEC.Transcriptomes, SomaticCancerAlterations
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