ggmsa

DOI: 10.18129/B9.bioc.ggmsa    

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

Plot Multiple Sequence Alignment using 'ggplot2'

Bioconductor version: Development (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

HTML R Script ggmsa
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization
Version 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
LinkingTo
Suggests ggtreeExtra, ggtree(>= 1.17.1), ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0), phangorn
SystemRequirements
Enhances
URL http://yulab-smu.top/ggmsa/
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) ggmsa_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ggmsa
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggmsa
Package Short Url https://bioconductor.org/packages/ggmsa/
Package Downloads Report Download Stats

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