Files in acorg/acutilsLite
A package for working with CPE databases
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/acdatabase_antigens.R
R/acdatabase_dbtest.R
R/acdatabase_experiments.R
R/acdatabase_merging.R
R/acdatabase_methods.R
R/acdatabase_names.R
R/acdatabase_passage.R
R/acdatabase_sequences.R
R/acdatabase_sera.R
R/acdatabase_titertables.R
R/acdatabase_utils.R
R/acdatabases_plot.R
R/constants.R
README.Rmd
README.md
acutilsLite.Rproj
man/ac.exp.Rd
man/ac.inGroups.Rd
man/acdb.applyFunction.Rd
man/acdb.as.list.Rd
man/acdb.extract.Rd
man/acdb.find.Rd
man/acdb.getIDs.Rd
man/acdb.idToAttr.Rd
man/acdb.matchNames.Rd
man/acdb.matchNamesIndices.Rd
man/acdb.matchSubstitutions.Rd
man/acdb.matchSubstitutionsIndices.Rd
man/acdb.nameIDs.Rd
man/acdb.search.Rd
man/acdb.slice.Rd
man/acids.applyFunction.Rd
man/ag.Rd
man/ag.attribute.Rd
man/ag.children.Rd
man/ag.clade.Rd
man/ag.clade.self.Rd
man/ag.cluster.Rd
man/ag.descendents.Rd
man/ag.descendentsTree.Rd
man/ag.duplicate.Rd
man/ag.experiments.Rd
man/ag.inheritance.Rd
man/ag.long.Rd
man/ag.parent.Rd
man/ag.passageChildren.Rd
man/ag.passageChildrenFlat.Rd
man/ag.passageChildrenTree.Rd
man/ag.passageInheritance.Rd
man/ag.passageParent.Rd
man/ag.passageSiblings.Rd
man/ag.root.Rd
man/ag.sequence.allVariants.Rd
man/ag.sequence.calculate.Rd
man/ag.sequence.pluck.Rd
man/ag.short.Rd
man/ag.standardlong.Rd
man/ag.substitutions.Rd
man/agdb.Rd
man/agdb.ag.Rd
man/agdb.alterations.Rd
man/agdb.append.Rd
man/agdb.checkAG.Rd
man/agdb.checkagdb.Rd
man/agdb.checkalterations.Rd
man/agdb.checkgenes.Rd
man/agdb.checkid.Rd
man/agdb.checkisolation.Rd
man/agdb.checkpassage.Rd
man/agdb.clusters.Rd
man/agdb.experiments.Rd
man/agdb.genes.Rd
man/agdb.getIDs.Rd
man/agdb.hasSubstitutions.Rd
man/agdb.homologousSera.Rd
man/agdb.id.Rd
man/agdb.isolation.Rd
man/agdb.merge.Rd
man/agdb.new.Rd
man/agdb.passage.Rd
man/agdb.sequencesFromMap.Rd
man/agdb.substitutions.Rd
man/agid.cluster.Rd
man/as.list.acdatabase.ag.Rd
man/cash-.acdatabase.entry.Rd
man/check_condition.Rd
man/collate.Rd
man/combineTiters.Rd
man/expdb.Rd
man/expdb.ags.Rd
man/expdb.merge.Rd
man/expdb.sr.Rd
man/expdb.toLongTibble.Rd
man/exper.merge.Rd
man/exper.toLongTibble.Rd
man/grapes-cash-grapes-set.Rd
man/grapes-cash-grapes.Rd
man/h3_clade_grouping_heirarchy.Rd
man/h3_clade_order.Rd
man/is.substitution.Rd
man/logtiter.toPlot.Rd
man/longtiters.addRecords.Rd
man/longtiters.colbase.Rd
man/longtiters.plotdata.Rd
man/mergeTiters.Rd
man/outbox.agdb.database.Rd
man/outbox.srdb.Rd
man/place_abvs.Rd
man/print.acdatabase.entry.Rd
man/read.agdb.Rd
man/read.srdb.Rd
man/result.titerTable.Rd
man/sequences_plot.Rd
man/sr.Rd
man/sr.attribute.Rd
man/sr.children.Rd
man/sr.cluster.Rd
man/sr.experiments.Rd
man/sr.inheritance.Rd
man/sr.parent.Rd
man/srdb.Rd
man/srdb.append.Rd
man/srdb.clusters.Rd
man/srdb.getIDs.Rd
man/srdb.homologousAntigens.Rd
man/srdb.id.Rd
man/srdb.matchAnimalIDs.Rd
man/srdb.matchAnimalIDsIndices.Rd
man/srdb.merge.Rd
man/srdb.new.Rd
man/srdb.sr.Rd
man/srid.cluster.Rd
man/standardizeStrainName.Rd
man/standardizeStrainNames.Rd
man/sub-.acdatabase.entry.Rd
man/subs.split.Rd
man/summarise_plotdata_by_ag_cluster.Rd
man/summarise_plotdata_by_sr_cluster.Rd
man/tibble.factorize.Rd
man/titer.toLog.Rd
man/titer.toPrint.Rd
man/titers.getThresholds.Rd
man/titers.toNumeric.Rd
man/write.agdb.Rd
man/write.srdb.Rd
tests/testthat.R
tests/testthat/.DS_Store
tests/testthat/test-acdatabase_antigens.R
tests/testthat/test-acdatabase_functions.R
tests/testthat/test-acdatabase_utils.R
tests/testthat/testdata/agdbB.json
tests/testthat/testdata/agdb_h3_small.json
tests/testthat/testdata/bags.RData
