ggmsa
Plot Multiple Sequence Alignment using 'ggplot2'
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggmsa")Details
| Maintainer | Guangchuang Yu <guangchuangyu@gmail.com> |
| Author | Guangchuang Yu [aut, cre, ths] (ORCID: <https://orcid.org/0000-0002-6485-8781>), Lang Zhou [aut], Shuangbin Xu [ctb], Huina Huang [ctb] |
| License | Artistic-2.0 |
| URL | https://doi.org/10.1093/bib/bbac222(paper), https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/ (book) |
| Bug Reports | https://github.com/YuLab-SMU/ggmsa/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/ggmsa/ |
Citation
From within R, enter citation("ggmsa"):
Guangchuang Yu, Lang Zhou. ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'. doi:10.18129/B9.bioc.ggmsa, R package version 1.18.0, https://bioconductor.org/packages/ggmsa.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ggmsa_1.18.0.tar.gz |
| Windows binary (x86_64) | ggmsa_1.18.0.zip |
| macOS binary (arm64) | ggmsa_1.18.0.tgz |
| macOS binary (x86_64) | ggmsa_1.18.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1)
Suggests: ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat (>= 3.0.0), yulab.utils
Reverse dependencies
Imports Me (1): ggaligner