Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019)

Documentation for package ‘CovidMutations’ version 0.1.3

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