README.md

In philliplab/ViralHaplotyper: Viral Haplotyper

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: * Each unique sequences forms a haplotype * All the sequences together forms a single haplotype * ... (Use clustering / phylogenetic techniques?)

Furthermore, this package provides tools that one can use to inspect a haplotype: * List all unique sequences * Plot a phylogenetic tree of the haplotype * Find outliers in the haplotype * Find the consensus sequence of the haplotype * ...

Lastly, given a list of haplotypes, certain summaries can be reported: * Table of haplotypes sorted on different criteria like: * Number of unique sequences * Total number of sequences

philliplab/ViralHaplotyper documentation built on May 25, 2019, 5:05 a.m.