ViralHaplotyper is a tool for investigating the haplotypes present in a dataset.
It can be installed directly from github using devtools. In an R session issue these commands:
local({r <- getOption("repos")
r["CRAN"] <- "http://cran.rstudio.com"
options(repos=r)
})
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings", ask=FALSE)
install.packages('devtools')
library(devtools)
install_github('rstudio/shiny')
install_github('philliplab/ViralHaplotyper')
To run the web UI from within an R session:
library(ViralHaplotyper)
run_ViralHaplotyper_app()
To run the web UI from the commandline:
R -e 'library(ViralHaplotyper); run_ViralHaplotyper_app()'
Given a dataset, it can construct haplotypes for the dataset using these techniques:
Furthermore, this package provides tools that one can use to inspect a haplotype:
Lastly, given a list of haplotypes, certain summaries can be reported: