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
longreadvqs_0.1.3.zip(r-4.5)longreadvqs_0.1.3.zip(r-4.4)longreadvqs_0.1.3.zip(r-4.3)
longreadvqs_0.1.3.tgz(r-4.4-any)longreadvqs_0.1.3.tgz(r-4.3-any)
longreadvqs_0.1.3.tar.gz(r-4.5-noble)longreadvqs_0.1.3.tar.gz(r-4.4-noble)
longreadvqs_0.1.3.tgz(r-4.4-emscripten)longreadvqs_0.1.3.tgz(r-4.3-emscripten)
longreadvqs.pdf |longreadvqs.html✨
longreadvqs/json (API)
NEWS

Peer review:

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

On CRAN:

13 exports 1.39 score 100 dependencies 4 scripts 130 downloads

Last updated 22 days agofrom:4d87b4c0b2. Checks:OK: 7. Indexed: yes.

Exports:%>%AAcomparefiltfastgapremoveotucomparepctoptsnvcomparevqsassessvqscomparevqscustompctvqsoutvqsresubvqssub

Dependencies:abindade4apeaskpassbackportsBiocGenericsBiostringsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11crayoncurlDerivdigestdoBydplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataggplot2ggpubrggrepelggsciggsignifglueGPArotationgridExtragtablehttrIRangesisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamnormtmodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpixmappkgconfigplyrpolynompsychpurrrpwalignQSutilsquantregR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrstatixS4VectorsscalessegmentedseqinrspSparseMstringdiststringistringrsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc