ggmsa

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ggmsa.

Plot Multiple Sequence Alignment using 'ggplot2'

Bioconductor version: 3.14

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 "4.1") 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization

Version 1.0.0

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

System Requirements

URL http://yulab-smu.top/ggmsa/

Bug Reports https://github.com/YuLab-SMU/ggmsa/issues

Suggests ggtreeExtra, ggtree(>= 1.17.1), ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0), phangorn

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Package Archives

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

Source Package ggmsa_1.0.0.tar.gz

Windows Binary ggmsa_1.0.0.zip

macOS 10.13 (High Sierra) ggmsa_1.0.0.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

Old Source Packages for BioC 3.14 Source Archive