Package: longreadvqs 0.1.5

longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing Data

Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2026) <doi:10.1371/journal.pcbi.1014208>] 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.

Authors:Nakarin Pamornchainavakul [aut, cre]

longreadvqs_0.1.5.tar.gz
longreadvqs_0.1.5.zip(r-4.7-any)longreadvqs_0.1.5.zip(r-4.6-any)longreadvqs_0.1.5.zip(r-4.5-any)
longreadvqs_0.1.5.tgz(r-4.6-any)longreadvqs_0.1.5.tgz(r-4.5-any)
longreadvqs_0.1.5.tar.gz(r-4.7-any)longreadvqs_0.1.5.tar.gz(r-4.6-any)
longreadvqs_0.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
longreadvqs/json (API)

# Install 'longreadvqs' in R:

install.packages('longreadvqs', repos = c('https://nakarinp.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nakarinp/longreadvqs/issues

On CRAN:

4.18 score 1 stars 4 scripts 346 downloads 13 exports 98 dependencies

Last updated from:bb24b5dfc3. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	249
source / vignettes	OK	377
linux-release	OK	224
macos-release	OK	256
macos-oldrel	OK	190
windows-devel	OK	174
windows-release	OK	178
windows-oldrel	OK	181
wasm-release	OK	171

Exports:%>%AAcompare filtfast gapremove otucompare pctopt snvcompare vqsassess vqscompare vqscustompct vqsout vqsresub vqssub

Dependencies:abind ade4 ape backports BiocGenerics Biostrings boot broom car carData cli colorspace corrplot cowplot cpp11 crayon Deriv digest doBy dplyr farver forecast Formula fracdiff generics ggplot2 ggpubr ggrepel ggsci ggsignif glue GPArotation gridExtra gtable IRanges isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mgcv minqa mnormt modelr nlme nloptr nnet numDeriv pbkrtest pillar pixmap pkgconfig plyr polynom psych purrr pwalign QSutils quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rstatix S4Vectors S7 scales segmented Seqinfo seqinr sp SparseM stringdist stringi stringr survival tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr XVector zoo

Comparing viral quasispecies with longreadvqs

Rendered fromlongreadvqs-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-04-28
Started: 2024-03-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Comparing viral quasispecies diversity metrics at amino acid level	AAcompare
Filtering highly dissimilar reads/sequences out of the alignment	filtfast
Removing gap-rich positions and/or reads/sequences	gapremove
Comparing operational taxonomic unit (OTU) by k-means clustering between samples	otucompare
Optimizing cut-off percentage for noise minimization	pctopt
Plotting single nucleotide variant (SNV) frequency in read alignment across different samples	snvcompare
Sequencing error and noise minimization, read down-sampling, and data preparation for viral quasispecies comparison	vqsassess
Comparing viral quasispecies profile and operational taxonomic unit (OTU) classified by k-means clustering between samples	vqscompare
Sequencing error and noise minimization with customized % cut-off at particular nucleotide region, read down-sampling, and data preparation for viral quasispecies comparison	vqscustompct
Exporting viral quasispecies profile comparison results	vqsout
Computing viral quasispecies diversity metrics of noise-minimized repeatedly down-sampled read alignments	vqsresub
Computing viral quasispecies diversity metrics of noise-minimized down-sampled read alignment	vqssub