ggmsa

DOI: 10.18129/B9.bioc.ggmsa  

Plot Multiple Sequence Alignment using 'ggplot2'

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	ggmsa
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 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)
LinkingTo
Suggests	ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://doi.org/10.1093/bib/bbac222(paper) https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/(book)
BugReports	https://github.com/YuLab-SMU/ggmsa/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ggmsa_1.4.0.tar.gz
Windows Binary	ggmsa_1.4.0.zip
macOS Binary (x86_64)	ggmsa_1.4.0.tgz
macOS Binary (arm64)	ggmsa_1.4.0.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