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ggmsa

This is the development version of ggmsa; for the stable release version, see ggmsa.

Plot Multiple Sequence Alignment using 'ggplot2'


Bioconductor version: Development (3.19)

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 (from within R, enter citation("ggmsa")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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)
System Requirements
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
Suggests ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me ggaligner, SeedMatchR
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package ggmsa_1.9.0.tar.gz
Windows Binary ggmsa_1.9.0.zip
macOS Binary (x86_64) ggmsa_1.9.0.tgz
macOS Binary (arm64) ggmsa_1.9.0.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