Multiple Sequence Alignment for R Shiny

Visualises multiple sequence alignments dynamically within the Shiny web application framework.


msaR is a an htmlwidgets wrapper of the BioJS MSA viewer javascript library. msa will pass alignments to the BioJS MSA and has a convenience function that will handle the following formats:

  1. A character string which is interpreted to be a fasta file (opened by ape::read.dna)
  2. A DNAbin class object (ape)
  3. An XStringSet (Biostrings) including "DNAStringSet", "RNAStringSet", "AAStringSet", and "BStringSet"
  4. An XMultiple Alignment (Biostings) including "DNAMultipleAlignment","RNAMultipleAlignment", and"AAMultipleAlignment"

Any of these types of objects can be passed to msaR to create an html widget. This package in not on CRAN/Bioconductor and can be installed using devtools. See the online docs for an interactive version of this widget.

#devtools::install_github('zachcp/msaR')
 
library(msaR)
 
# read some sequences from a multiple sequence alignment file and display
seqfile <- system.file("sequences","AHBA.aln",package="msaR")
msaR(seqfile)

msaR can be used as a widget with the Shiny web application framework.

In ui.R

msaROutput("msa", width="100%")

In server.R

output$msa <- renderMsaR(
  msaR(seqfile)
)

All contributions are welcome! Please feel free to submit a pull request.

If you have any problem or suggestion please open an issue here

This project is licensed under the Boost Software License 1.0.

If you use the MSAViewer on your website, it solely requires you to link to us

News

NEWS

0.1.0 Basic Release to CRAN

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("msaR")

0.2.0 by Zachary Charlop-Powers, 4 months ago


Browse source code at https://github.com/cran/msaR


Authors: Benedikt Rauscher [aut, cph], Zachary Charlop-Powers [cre, aut]


Documentation:   PDF Manual  


BSL-1.0 license


Imports ape, htmlwidgets

Suggests Biostrings, knitr, rmarkdown


See at CRAN