CRAN/E | longreadvqs

longreadvqs

Viral Quasispecies Comparison from Long-Read Sequencing Data

Installation

About

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.

github.com/NakarinP/longreadvqs
Bug report File report

Key Metrics

Version 0.1.2
R ≥ 2.10
Published 2024-04-14 156 days ago
Needs compilation? no
License GPL-3
CRAN checks longreadvqs results

Downloads

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Maintainer

Maintainer

Nakarin Pamornchainavakul

Authors

Nakarin Pamornchainavakul

aut / cre

Material

README
NEWS
Reference manual
Package source

Vignettes

longreadvqs-vignette

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-develnot available

x86_64

r-releasenot available

x86_64

r-oldrelnot available

x86_64

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