Welcome to the new bioconductor.org!

ggbio

Visualization tools for genomic data


Bioconductor version: Release (3.18)

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 1.50.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
System Requirements
URL https://lawremi.github.io/ggbio/
Bug Reports https://github.com/lawremi/ggbio/issues
See More
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
Linking To
Enhances
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 Build Report

Package Archives

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

Source Package ggbio_1.50.0.tar.gz
Windows Binary ggbio_1.50.0.zip (64-bit only)
macOS Binary (x86_64) ggbio_1.50.0.tgz
macOS Binary (arm64) ggbio_1.50.0.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
Old Source Packages for BioC 3.18 Source Archive