ggbio
Visualization tools for genomic data
Bioconductor version: 3.23 · Package version: 1.60.0
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
| Maintainer | Michael Lawrence <lawremi@gmail.com> |
| Author | Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Sanchit Saini [ctb], Johannes Rainer [ctb] |
| License | Artistic-2.0 |
| URL | https://lawremi.github.io/ggbio/ |
| Bug Reports | https://github.com/lawremi/ggbio/issues |
| Downloads rank | 3288 |
| Source branch | RELEASE_3_23 |
| biocViews | Infrastructure, Software, Visualization |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ggbio_1.60.0.tar.gz |
| Windows binary (x86_64) | ggbio_1.60.0.zip |
| macOS binary (arm64) | ggbio_1.60.0.tgz |
| macOS binary (x86_64) | ggbio_1.60.0.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 (13): BOBaFIT, cageminer, Damsel, derfinderPlot, GenomicOZone, msgbsR, PopPsiSeqR, R3CPET, ReportingTools, RiboProfiling, scafari, scruff, SomaticSignatures
Suggests Me (15): bambu, beadarray, ensembldb, FRASER, gwascat, NanoporeRNASeq, NanoStringNCTools, OUTRIDER, regionReport, RnBeads, shiny.gosling, Single.mTEC.Transcriptomes, SomaticCancerAlterations, StructuralVariantAnnotation, universalmotif