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://msq-123.r-universe.dev', 'https://cloud.r-project.org'))

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 152 downloads 12 exports 79 dependencies

Last updated 4 years agofrom:b4521bdd86. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 18 2024
R-4.5-win	OK	Oct 18 2024
R-4.5-linux	OK	Oct 18 2024
R-4.4-win	OK	Oct 18 2024
R-4.4-mac	OK	Oct 18 2024
R-4.3-win	OK	Oct 18 2024
R-4.3-mac	OK	Oct 18 2024

Exports:AssayMutRatio doubleAssay globalProteinMut globalSNPprofile indelSNP LastfiveNrMutation mergeEvents MutByGene mutStat nucmerRMD plotMutAnno plotMutProteins

Dependencies:abind ade4 backports boot broom car carData cli colorspace corrplot cowplot cpp11 Deriv doBy dplyr fansi farver formatR Formula futile.logger futile.options generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable isoband labeling lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa modelr munsell nlme nloptr nnet numDeriv pbkrtest pillar pixmap pkgconfig polynom purrr quantreg R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang rstatix scales segmented seqinr sp SparseM stringi stringr survival tibble tidyr tidyselect utf8 vctrs VennDiagram viridisLite withr

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

Shaoqian Ma, Yongyou Zhang

Rendered fromvignette.Rmdusingknitr::rmarkdownon Oct 18 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate the mutation detection rate using different assays	AssayMutRatio
Assays for mutation detection using different primers and probes	assays
A list of places in China	chinalist
Mutation annotation results produced by "indelSNP" function	covid_annot
Detection of co-occurring mutations using double-assay information	doubleAssay
"GFF3" format gene position data for SARS-Cov-2	gene_position
"GFF3" format annotation data for SARS-Cov-2	gff3
Global mutational events profiling of proteins	globalProteinMut
Global single nucleotide polymorphism (SNP) profiling in virus genome	globalSNPprofile
Provide effects of each single nucleotide polymorphism (SNP), insertion and deletion in virus genome	indelSNP
Bacth assay analysis for last five Nr of primers	LastfiveNrMutation
Merge neighboring events of single nucleotide polymorphism (SNP), insertion and deletion.	mergeEvents
Plot mutation counts for certain genes	MutByGene
Plot mutation statistics for nucleiotide	mutStat
Mutation information derived from "nucmer" SNP analysis	nucmer
Preprocessed "nucmer.snpss" file using "nucmerRMD" function	nucmerr
Preprocess "nucmer" object to add group information	nucmerRMD
Plot the mutation statistics after annotating the "nucmer" object by "indelSNP" function	plotMutAnno
Plot the most frequent mutational events for proteins in the SARS-CoV-2 genome	plotMutProteins
SARS-Cov-2 genomic reference sequence from NCBI	refseq