Package: longreadvqs 0.1.3

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.

Authors:Nakarin Pamornchainavakul [aut, cre]

longreadvqs_0.1.3.tar.gz
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longreadvqs_0.1.3.tgz(r-4.4-any)longreadvqs_0.1.3.tgz(r-4.3-any)
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longreadvqs.pdf |longreadvqs.html✨
longreadvqs/json (API)
NEWS

# 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:

4.65 score 4 scripts 150 downloads 13 exports 101 dependencies

Last updated 3 months agofrom:4d87b4c0b2. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-win	OK	Oct 26 2024
R-4.5-linux	OK	Oct 26 2024
R-4.4-win	OK	Oct 26 2024
R-4.4-mac	OK	Oct 26 2024
R-4.3-win	OK	Oct 26 2024
R-4.3-mac	OK	Oct 26 2024

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

Dependencies:abind ade4 ape askpass backports BiocGenerics Biostrings boot broom car carData cli colorspace corrplot cowplot cpp11 crayon curl Deriv digest doBy dplyr fansi farver Formula generics GenomeInfoDb GenomeInfoDbData ggplot2 ggpubr ggrepel ggsci ggsignif glue GPArotation gridExtra gtable httr IRanges isoband jsonlite labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mgcv microbenchmark mime minqa mnormt modelr munsell nlme nloptr nnet numDeriv openssl pbkrtest pillar pixmap pkgconfig plyr polynom psych purrr pwalign QSutils quantreg R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang rstatix S4Vectors scales segmented seqinr sp SparseM stringdist stringi stringr survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Comparing viral quasispecies with longreadvqs

Nakarin Pamornchainavakul, DVM, PhD

Rendered fromlongreadvqs-vignette.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-08-25
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