ggbio

Visualization tools for genomic data

Bioconductor version: Release (3.17)

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 "4.3") 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")

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

Details

biocViews	Infrastructure, Software, Visualization
Version	1.48.0
In Bioconductor since	BioC 2.9 (R-2.14) (12 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
Linking To
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
System Requirements
Enhances
URL	https://lawremi.github.io/ggbio/
Bug Reports	https://github.com/lawremi/ggbio/issues

Depends On Me	CAFE, intansv
Imports Me	BOBaFIT, cageminer, derfinderPlot, FLAMES, 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_1.48.0.tar.gz
Windows Binary	ggbio_1.48.0.zip
macOS Binary (x86_64)	ggbio_1.48.0.tgz
macOS Binary (arm64)	ggbio_1.48.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ggbio
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ggbio
Bioc Package Browser	https://code.bioconductor.org/browse/ggbio/
Package Short Url	https://bioconductor.org/packages/ggbio/
Package Downloads Report	Download Stats