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ggbio

Visualization tools for genomic data

Bioconductor version: 3.24 · Package version: 1.61.0

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.

Installation

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

BiocManager::install("ggbio")

Details

MaintainerMichael Lawrence <lawremi@gmail.com>
AuthorTengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Sanchit Saini [ctb], Johannes Rainer [ctb]
LicenseArtistic-2.0
URLhttps://lawremi.github.io/ggbio/
Bug Reportshttps://github.com/lawremi/ggbio/issues
Downloads rank3288
Source branchdevel
biocViewsInfrastructure, Software, Visualization

Download

Follow the installation instructions to use this package in your R session.

Source packageggbio_1.61.0.tar.gz
Windows binary (x86_64)ggbio_1.61.0.zip
macOS binary (arm64)ggbio_1.61.0.tgz
macOS binary (x86_64)ggbio_1.61.0.tgz
Dependencies

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), Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), BSgenome (>= 1.77.1), VariantAnnotation (>= 1.55.1), rtracklayer (>= 1.69.1), GenomicFeatures (>= 1.61.4), OrganismDbi, ensembldb (>= 2.33.1), AnnotationDbi, AnnotationFilter, rlang

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

Reverse dependencies

Depends On Me (2): CAFE, intansv

Imports Me (12): BOBaFIT, cageminer, Damsel, derfinderPlot, GenomicOZone, msgbsR, PopPsiSeqR, R3CPET, ReportingTools, scafari, scruff, SomaticSignatures

Suggests Me (15): bambu, beadarray, ensembldb, FRASER, gwascat, NanoporeRNASeq, NanoStringNCTools, OUTRIDER, regionReport, RnBeads, shiny.gosling, Single.mTEC.Transcriptomes, SomaticCancerAlterations, StructuralVariantAnnotation, universalmotif