ggmsa
Plot Multiple Sequence Alignment using 'ggplot2'
Bioconductor version: Release (3.17)
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.
Author: Lang Zhou [aut, cre], Guangchuang Yu [aut, ths] 
, Shuangbin Xu [ctb], Huina Huang [ctb]
Maintainer: Lang Zhou <nyzhoulang at gmail.com>
citation("ggmsa")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggmsa")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("ggmsa")| ggmsa | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| Imports | Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree(>= 1.17.1) |
| Linking To | |
| Suggests | ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) |
| System Requirements | |
| Enhances | |
| 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 |
See More
| Depends On Me | |
| Imports Me | ggaligner, SeedMatchR |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ggmsa_1.6.0.tar.gz |
| Windows Binary | ggmsa_1.6.0.zip |
| macOS Binary (x86_64) | ggmsa_1.6.0.tgz |
| macOS Binary (arm64) | ggmsa_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ggmsa |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ggmsa |
| Bioc Package Browser | https://code.bioconductor.org/browse/ggmsa/ |
| Package Short Url | https://bioconductor.org/packages/ggmsa/ |
| Package Downloads Report | Download Stats |