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Bioconductor - ggbio (development version)

ggbio

This is the development version of ggbio; for the stable release version, see ggbio.

Visualization tools for genomic data

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.57.1 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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), 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, GGally, ensembldb(>= 2.33.1), 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, Damsel, derfinderPlot, FLAMES, GenomicOZone, msgbsR, R3CPET, ReportingTools, RiboProfiling, scruff, SomaticSignatures, OHCA Suggests Me bambu, beadarray, ensembldb, FRASER, gwascat, interactiveDisplay, NanoStringNCTools, OUTRIDER, regionReport, RnBeads, shiny.gosling, StructuralVariantAnnotation, universalmotif, NanoporeRNASeq, Single.mTEC.Transcriptomes, SomaticCancerAlterations Links To Me Build Report Build Report Package Archives

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

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