Performs variety of viral quasispecies diversity analyses [see Gregori et al. (2016) <doi:10.1016/j.virol.2016.03.017>] based on long-read sequence alignment. Main functions include 1) sequencing error minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.
Version: |
0.1.2 |
Depends: |
R (≥ 2.10) |
Imports: |
ape, Biostrings, cowplot, dplyr, ggplot2, ggpubr, grDevices, magrittr, plyr, purrr, QSutils, RColorBrewer, reshape2, scales, seqinr, stats, stringdist, stringr, tibble, tidyr |
Suggests: |
knitr, rmarkdown, testthat (≥ 3.0.0) |
Published: |
2024-04-14 |
DOI: |
10.32614/CRAN.package.longreadvqs |
Author: |
Nakarin Pamornchainavakul
[aut, cre] |
Maintainer: |
Nakarin Pamornchainavakul <pamornakarin at gmail.com> |
BugReports: |
https://github.com/NakarinP/longreadvqs/issues |
License: |
GPL-3 |
URL: |
https://github.com/NakarinP/longreadvqs |
NeedsCompilation: |
no |
Materials: |
README NEWS |
CRAN checks: |
longreadvqs results |