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
Browse package contents
Package details |
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| Author | Sandeep J. Joseph and Ben Li |
| Maintainer | Sandeep J. Joseph<sandeepjoseph@emory.edu> and Ben Li<ben.li@emory.edu> |
| License | GPL-2 |
| Version | 1.0 |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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