Bioconductor - ggbio

Bioconductor - ggbio
Bioconductor 3.22
Software Packages
ggbio
ggbio
This is the
released
version of ggbio; for the devel version, see
ggbio
Visualization tools for genomic data
DOI:
10.18129/B9.bioc.ggbio
Bioconductor version:
Release (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
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")

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
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
Infrastructure
Software
Visualization
Version
1.58.0
In Bioconductor since
BioC 2.9 (R-2.14) (14.5 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
ensembldb
(>= 2.33.1),
AnnotationDbi
AnnotationFilter
rlang
System Requirements
URL
Bug Reports
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
scafari
scruff
SomaticSignatures
, OHCA,
PopPsiSeqR
TmCalculator
Suggests Me
bambu
beadarray
ensembldb
FRASER
gwascat
interactiveDisplay
NanoStringNCTools
OUTRIDER
regionReport
RnBeads
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_1.58.0.tar.gz
Windows Binary (x86_64)
ggbio_1.58.0.zip
(64-bit only)
macOS Binary (x86_64)
ggbio_1.58.0.tgz
macOS Binary (arm64)
ggbio_1.58.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/ggbio
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/ggbio
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