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 [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 resultsRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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