Man pages for CovidMutations
Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019)
| AssayMutRatio | Calculate the mutation detection rate using different assays |
| assays | Assays for mutation detection using different primers and... |
| 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... |
| 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... |
| indelSNP | Provide effects of each single nucleotide polymorphism (SNP),... |
| LastfiveNrMutation | Bacth assay analysis for last five Nr of primers |
| mergeEvents | Merge neighboring events of single nucleotide polymorphism... |
| 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"... |
| plotMutProteins | Plot the most frequent mutational events for proteins in the... |
| refseq | SARS-Cov-2 genomic reference sequence from NCBI |
