ggmsa:a visual exploration tool for multiple sequence alignment and associated data
ggmsa
is designed for visualization and annotation of multiple
sequence alignment. It implements functions to visualize
publication-quality multiple sequence alignments (protein/DNA/RNA) in R
extremely simple and powerful.
For details, please visit http://yulab-smu.top/ggmsa/
๐จ Installation
The released version from Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggmsa")
Alternatively, you can grab the development version from github using devtools:
if (!requireNamespace("devtools", quietly=TRUE))
install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")
๐ก Quick Example
library(ggmsa)
protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")
ggmsa(protein_sequences, start = 221, end = 280, char_width = 0.5, seq_name = TRUE) + geom_seqlogo() + geom_msaBar()
๐ Learn more
Check out the guides for learning everything there is to know about all the different features:
๐ Author
- Guangchuang Yu Professor, PI
- Lang Zhou Masterโs Student
- Shuangbin Xu PhD Student
YuLab https://yulab-smu.top/
Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University
๐ Contributing
We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.