API for acorg/acutilsLite
A package for working with CPE databases
| Global functions | |
|---|---|
| $.acdatabase.entry | Man page |
| %$% | Man page |
| %$%<- | Man page |
| [.acdatabase.entry | Man page |
| `$.acdatabase.entry` | Source code |
| `%$%<-` | Source code |
| `%$%` | Source code |
| `[.acdatabase.entry` | Source code |
| aa.colors | Source code |
| aa.values | Source code |
| ac.exp | Man page |
| ac.inGroups | Man page Source code |
| acdb.applyFunction | Man page Source code |
| acdb.as.list | Man page Source code |
| acdb.extract | Man page Source code |
| acdb.find | Man page Source code |
| acdb.getIDs | Man page Source code |
| acdb.idToAttr | Man page Source code |
| acdb.inGroups | Source code |
| acdb.long | Source code |
| acdb.matchNames | Man page Source code |
| acdb.matchNamesIndices | Man page Source code |
| acdb.matchSubstitutions | Man page Source code |
| acdb.matchSubstitutionsIndices | Man page Source code |
| acdb.nameIDs | Man page Source code |
| acdb.search | Man page Source code |
| acdb.slice | Man page Source code |
| acids.applyFunction | Man page Source code |
| ag | Man page |
| ag.attribute | Man page Source code |
| ag.children | Man page Source code |
| ag.clade | Man page Source code |
| ag.clade.self | Man page Source code |
| ag.cluster | Man page Source code |
| ag.descendents | Man page Source code |
| ag.descendentsTree | Man page Source code |
| ag.duplicate | Man page Source code |
| ag.experiments | Man page Source code |
| ag.inResults | Source code |
| ag.inheritance | Man page Source code |
| ag.inheritance.variants | Source code |
| ag.inheritedPassageHistory | Source code |
| ag.long | Man page Source code |
| ag.parent | Man page Source code |
| ag.passageChildren | Man page Source code |
| ag.passageChildrenFlat | Man page Source code |
| ag.passageChildrenTree | Man page Source code |
| ag.passageIncludesEgg | Source code |
| ag.passageInheritance | Man page Source code |
| ag.passageParent | Man page Source code |
| ag.passageSiblings | Man page Source code |
| ag.root | Man page Source code |
| ag.sequence.allVariants | Man page Source code |
| ag.sequence.applySubs | Source code |
| ag.sequence.auto | Source code |
| ag.sequence.calculate | Man page Source code |
| ag.sequence.pluck | Man page Source code |
| ag.sequence.pluckFromID | Source code |
| ag.short | Man page Source code |
| ag.standardlong | Man page Source code |
| ag.substitutions | Man page Source code |
| agdb | Man page |
| agdb.ag | Man page Source code |
| agdb.alterations | Man page Source code |
| agdb.append | Man page Source code |
| agdb.checkAG | Man page Source code |
| agdb.checkagdb | Man page Source code |
| agdb.checkalterations | Man page Source code |
| agdb.checkgenes | Man page Source code |
| agdb.checkid | Man page Source code |
| agdb.checkisolation | Man page Source code |
| agdb.checkpassage | Man page Source code |
| agdb.clusters | Man page Source code |
| agdb.experiments | Man page Source code |
| agdb.genes | Man page Source code |
| agdb.getIDs | Man page Source code |
| agdb.getOrder | Source code |
| agdb.getRank | Source code |
| agdb.hasSubstitutions | Man page Source code |
| agdb.homologousSera | Man page Source code |
| agdb.id | Man page Source code |
| agdb.isolation | Man page Source code |
| agdb.loadTest | Source code |
| agdb.merge | Man page Source code |
| agdb.new | Man page Source code |
| agdb.passage | Man page Source code |
| agdb.root | Source code |
| agdb.sequencesFromMap | Man page Source code |
| agdb.short | Source code |
| agdb.substitutions | Man page Source code |
| agdb.year | Source code |
| agid.cluster | Man page Source code |
| as.list.acdatabase.ag | Man page Source code |
| check_condition | Man page Source code |
| clusters.colour | Source code |
| clusters.number | Source code |
| clusters.subsMatrix | Source code |
| clusters.toFactor | Source code |
| collate | Man page Source code |
| coloraa | Source code |
| combineTiters | Man page Source code |
| consensus | Source code |
| expdb | Man page |
| expdb.ags | Man page Source code |
| expdb.exp | Source code |
| expdb.expName | Source code |
| expdb.merge | Man page Source code |
| expdb.new | Source code |
| expdb.result | Source code |
| expdb.sr | Man page Source code |
| expdb.toLongTibble | Man page Source code |
| exper.merge | Man page Source code |
| exper.result.append | Source code |
| exper.toLongTibble | Man page Source code |
| extras.getYscale | Source code |
| extras.getYscaleFromTiters | Source code |
| extras.t_col | Source code |
| format_passage_history | Source code |
| geneseq.diff | Source code |
| get_agdb | Source code |
| get_expdb | Source code |
| get_protein_sequence | Source code |
| get_srdb | Source code |
| h3_clade_grouping_heirarchy | Man page |
| h3_clade_order | Man page |
| h3_clusters | Source code |
| is.substitution | Man page Source code |
| logtiter.toPlot | Man page |
| longtiters.addComparisonTiter | Source code |
| longtiters.addRecords | Man page Source code |
| longtiters.colbase | Man page Source code |
| longtiters.commonColumns | Source code |
| longtiters.getAbsentMuts | Source code |
| longtiters.labelRepeats | Source code |
| longtiters.merge | Source code |
| longtiters.order | Source code |
| longtiters.plotdata | Man page Source code |
| longtiters.splitSubstitutions | Source code |
| longtiters.subsTrafficLight | Source code |
| mergeTiters | Man page Source code |
| merge_on_passage | Source code |
| nucs_to_protein | Source code |
| outbox.agdb.database | Man page Source code |
| outbox.expdb | Source code |
| outbox.srdb | Man page Source code |
| place_abvs | Man page |
| print.acdatabase.entry | Man page Source code |
| print_and_capture | Source code |
| read.agdb | Man page Source code |
| read.expdb | Source code |
| read.expdbs | Source code |
| read.srdb | Man page Source code |
| result.titerTable | Man page Source code |
| seq_consensus | Source code |
| sequences_plot | Man page Source code |
| simpleCap | Source code |
| simpleTable | Source code |
| squaretiters.addNames | Source code |
| squaretiters.toLong | Source code |
| sr | Man page |
| sr.attribute | Man page Source code |
| sr.children | Man page Source code |
| sr.cluster | Man page Source code |
| sr.experiments | Man page Source code |
| sr.inResults | Source code |
| sr.inheritance | Man page Source code |
| sr.parent | Man page |
| srdb | Man page |
| srdb.append | Man page Source code |
| srdb.clusters | Man page Source code |
| srdb.getIDs | Man page Source code |
| srdb.getOrder | Source code |
| srdb.getRank | Source code |
| srdb.homologousAntigens | Man page Source code |
| srdb.id | Man page |
| srdb.matchAnimalIDs | Man page Source code |
| srdb.matchAnimalIDsIndices | Man page Source code |
| srdb.merge | Man page Source code |
| srdb.new | Man page Source code |
| srdb.sr | Man page Source code |
| srid.cluster | Man page Source code |
| standardise_db_name | Source code |
| standardizeStrainName | Man page Source code |
| standardizeStrainNames | Man page Source code |
| subs.split | Man page Source code |
| subs.split.list | Source code |
| summarise_plotdata_by_ag_cluster | Man page Source code |
| summarise_plotdata_by_sr_cluster | Man page Source code |
| tibble.factorize | Man page Source code |
| titer.toLog | Man page Source code |
| titer.toPrint | Man page Source code |
| titerplot.colourFacetLabels | Source code |
| titerplot.facet | Source code |
| titerplot.shadeClades | Source code |
| titerplot.styleaxes | Source code |
| titers.changeThreshold | Source code |
| titers.checkThresholds | Source code |
| titers.getThresholds | Man page Source code |
| titers.toNumeric | Man page Source code |
| titerscatter.coloured | Source code |
| titerscatter.faceted | Source code |
| toTable | Source code |
| trim_protein_sequence | Source code |
| unlist_safe | Source code |
| write.agdb | Man page Source code |
| write.expdb | Source code |
| write.srdb | Man page Source code |
