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longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing Data
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 |
| 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 |
Documentation:
Downloads:
Linking:
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https://CRAN.R-project.org/package=longreadvqs
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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