ggbio

DOI: 10.18129/B9.bioc.ggbio    

Visualization tools for genomic data

Bioconductor version: Release (3.14)

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 [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]

Maintainer: Michael Lawrence <michafla at gene.com>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggbio")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ggbio")

 

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

Details

biocViews Infrastructure, Software, Visualization
Version 1.42.0
In Bioconductor since BioC 2.9 (R-2.14) (10.5 years)
License Artistic-2.0
Depends methods, BiocGenerics, ggplot2 (>= 1.0.0)
Imports grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase(>= 1.29.2), Biobase, S4Vectors(>= 0.13.13), IRanges(>= 2.11.16), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.16), BSgenome, VariantAnnotation(>= 1.11.4), rtracklayer(>= 1.25.16), GenomicFeatures(>= 1.29.11), OrganismDbi, GGally, ensembldb(>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang
LinkingTo
Suggests vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex
SystemRequirements
Enhances
URL https://lawremi.github.io/ggbio/
BugReports https://github.com/lawremi/ggbio/issues
Depends On Me CAFE, intansv
Imports Me cageminer, derfinderPlot, GenomicOZone, msgbsR, R3CPET, ReportingTools, RiboProfiling, scruff, SomaticSignatures
Suggests Me bambu, beadarray, ensembldb, gwascat, interactiveDisplay, NanoporeRNASeq, NanoStringNCTools, Pi, regionReport, RnBeads, Single.mTEC.Transcriptomes, SomaticCancerAlterations, StructuralVariantAnnotation, universalmotif
Links To Me
Build Report  

Package Archives

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

Source Package ggbio_1.42.0.tar.gz
Windows Binary ggbio_1.42.0.zip
macOS 10.13 (High Sierra) ggbio_1.42.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ggbio
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggbio
Package Short Url https://bioconductor.org/packages/ggbio/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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