API for lerch-a/HaplotypR
HaplotypR, a pipeline to analyse amplicon deep sequencing genotyping data
| Global functions | |
|---|---|
| assignSNP | Source code |
| assignStrain | Source code |
| bindAmpliconReads | Source code |
| calculateMismatchFrequencies | Source code |
| callGenotype | Source code |
| callHaplotype | Source code |
| checkChimeras | Source code |
| clusterReads | Source code |
| compareDNAString | Source code |
| createContingencyTable | Source code |
| createFinalHaplotypTable | Source code |
| createFinalHaplotypTableDADA2 | Source code |
| createHaplotypOverviewTable | Source code |
| createProject | Source code |
| createSNPsList | Source code |
| demultiplexByMarker | Source code |
| demultiplexReads | Source code |
| extractSwarmClusterReads | Source code |
| findChimeras | Source code |
| flagChimera | Source code |
| getAppOptionDevel | Source code |
| getReferenceLocation | Source code |
| getReferenceSequence | Source code |
| mergeAmpliconReads | Source code |
| mergeMinIONfiles | Source code |
| plotHaplotypes | Source code |
| plotMismatchFrequencies | Source code |
| reclusterHaplotypesTable | Source code |
| removePrimer | Source code |
| renameDemultiplexedFiles | Source code |
| rmNreads | Source code Source code |
| runShinyApp | Source code |
| writeHaplotypList | Source code |
