README.md

In QSutils: Quasispecies Diversity

QSutils

Set of utility functions in viral quasispecies analysis with NGS data. Most are equally usefull in metagenomic studies. There are three main types of functions: (1) data manipulation and exploration; functions useful in converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and to visualize haplotype alignments. (2) diversity indices; functions to compute diversities and entropies; incidence, abundance and fuctional indices are considered. (3) data simulation; functions useful in generating random viral quasispecies data.

How to install the package

```{r,message=FALSE} library(devtools) install_git("https://github.com/VHIRHepatiques/QSutils")

library(QSutils) ```

QSutils documentation built on Nov. 8, 2020, 7:42 p.m.