Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.
Package details |
|
---|---|
Author | Mercedes Guerrero-Murillo [cre, aut] (<https://orcid.org/0000-0002-5556-2460>), Josep Gregori i Font [aut] (<https://orcid.org/0000-0002-4253-8015>) |
Bioconductor views | Alignment DNASeq DataImport GeneticVariability Genetics SequenceMatching Sequencing Software |
Maintainer | Mercedes Guerrero-Murillo <mergumu@gmail.com> |
License | file LICENSE |
Version | 1.8.0 |
Package repository | View on Bioconductor |
Installation |
Install the latest version of this package by entering the following in R:
|
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.