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
DOI: 10.32614/CRAN.package.longreadvqs
Author: Nakarin Pamornchainavakul ORCID iD [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


Reference manual: longreadvqs.pdf
Vignettes: longreadvqs-vignette


Package source: longreadvqs_0.1.2.tar.gz
Windows binaries: r-devel: longreadvqs_0.1.2.zip, r-release: longreadvqs_0.1.2.zip, r-oldrel: longreadvqs_0.1.2.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available


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