benliemory/BinStrain: Statistical modeling for SNP based genotyping of mixed bacterial strains

Uses a binomial model to describe the observed alternative allele (SNP) in a target genomic region (or the whole genome). A well-established two step method is used to estimate the proportion of serovar strain-specific SNPs present in pure or mixed infection of genotypes. First step is a direct estimate by using the sparsity of the design matrix. Quadratic optimization method is involved in the second step. Originally developed for direct sequencing of C. trachomatis from clinical samples.

Getting started

Package details

AuthorSandeep J. Joseph and Ben Li
MaintainerSandeep J. Joseph<sandeepjoseph@emory.edu> and Ben Li<ben.li@emory.edu>
LicenseGPL-2
Version1.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("benliemory/BinStrain")
benliemory/BinStrain documentation built on May 12, 2019, 12:14 p.m.