longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing Data

Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2024) <doi:10.21203/rs.3.rs-4637890/v1>] based on long-read sequence alignment. Main functions include 1) sequencing error and other noise minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.

Version: 0.1.3
Depends: R (≥ 2.10)
Imports: ape, Biostrings, cowplot, dplyr, ggplot2, ggpubr, grDevices, IRanges, magrittr, methods, plyr, purrr, QSutils, RColorBrewer, reshape2, scales, seqinr, stats, stringdist, stringr, tibble, tidyr
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2024-08-26
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

Documentation:

Reference manual: longreadvqs.pdf
Vignettes: longreadvqs-vignette (source, R code)

Downloads:

Package source: longreadvqs_0.1.3.tar.gz
Windows binaries: r-devel: longreadvqs_0.1.3.zip, r-release: longreadvqs_0.1.3.zip, r-oldrel: longreadvqs_0.1.3.zip
macOS binaries: r-devel (arm64): longreadvqs_0.1.3.tgz, r-release (arm64): longreadvqs_0.1.3.tgz, r-oldrel (arm64): not available, r-devel (x86_64): longreadvqs_0.1.3.tgz, r-release (x86_64): not available, r-oldrel (x86_64): not available
Old sources: longreadvqs archive

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