Package: CovidMutations 0.1.3

Shaoqian Ma

CovidMutations: Mutation Analysis and Assay Validation Toolkit for COVID-19 (Coronavirus Disease 2019)

A feasible framework for mutation analysis and reverse transcription polymerase chain reaction (RT-PCR) assay evaluation of COVID-19, including mutation profile visualization, statistics and mutation ratio of each assay. The mutation ratio is conducive to evaluating the coverage of RT-PCR assays in large-sized samples<doi:10.20944/preprints202004.0529.v1>.

Authors:Shaoqian Ma [aut, cre], Yongyou Zhang [aut]

CovidMutations_0.1.3.tar.gz
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CovidMutations.pdf |CovidMutations.html✨
CovidMutations/json (API)
NEWS

# Install 'CovidMutations' in R:
install.packages('CovidMutations', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/msq-123/covidmutations/issues

Datasets:
  • assays - Assays for mutation detection using different primers and probes
  • chinalist - A list of places in China
  • covid_annot - Mutation annotation results produced by "indelSNP" function
  • gene_position - "GFF3" format gene position data for SARS-Cov-2
  • gff3 - "GFF3" format annotation data for SARS-Cov-2
  • nucmer - Mutation information derived from "nucmer" SNP analysis
  • nucmerr - Preprocessed "nucmer.snpss" file using "nucmerRMD" function
  • refseq - SARS-Cov-2 genomic reference sequence from NCBI

On CRAN:

4.30 score 4 stars 6 scripts 186 downloads 12 exports 79 dependencies

Last updated 4 years agofrom:b4521bdd86. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winOKOct 10 2024
R-4.5-linuxOKOct 10 2024
R-4.4-winOKOct 10 2024
R-4.4-macOKOct 10 2024
R-4.3-winOKOct 10 2024
R-4.3-macOKOct 10 2024

Exports:AssayMutRatiodoubleAssayglobalProteinMutglobalSNPprofileindelSNPLastfiveNrMutationmergeEventsMutByGenemutStatnucmerRMDplotMutAnnoplotMutProteins

Dependencies:abindade4backportsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11DerivdoBydplyrfansifarverformatRFormulafutile.loggerfutile.optionsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpixmappkgconfigpolynompurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenrlangrstatixscalessegmentedseqinrspSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsVennDiagramviridisLitewithr

CovidMutations: a feasible framework for mutation analysis and assays validation of COVID-19

Shaoqian Ma, Yongyou Zhang

Rendered fromvignette.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2020-08-29
Started: 2020-08-17