ggbio
Visualization tools for genomic data
Bioconductor version: Release (3.20)
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("ggbio")):
Installation
To install this package, start R (version "4.4") 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 | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Infrastructure, Software, Visualization |
| Version | 1.54.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (13 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, Damsel, derfinderPlot, FLAMES, GenomicOZone, msgbsR, R3CPET, ReportingTools, RiboProfiling, scruff, SomaticSignatures, OHCA, MOCHA |
| 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.
| Source Package | ggbio_1.54.0.tar.gz |
| Windows Binary (x86_64) | ggbio_1.54.0.zip |
| macOS Binary (x86_64) | ggbio_1.54.0.tgz |
| macOS Binary (arm64) | ggbio_1.54.0.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 |