# Generated by roxygen2: do not edit by hand

export(CMdictionary)
export(CMoptions)
export(EntityFinder)
export(Onassis)
export(Similarity)
export(connectToGEODB)
export(dictTypes)
export(experiment_types)
export(filterTerms)
export(findHealthy)
export(getGEOMetadata)
export(listCMOptions)
export(listSimilarities)
export(organism_types)
exportClasses(Onassis)
exportClasses(Similarity)
exportMethods("CaseMatch<-")
exportMethods("FindAllMatches<-")
exportMethods("OrderIndependentLookup<-")
exportMethods("SearchStrategy<-")
exportMethods("Stemmer<-")
exportMethods("StopWords<-")
exportMethods("SynonymType<-")
exportMethods("dictInfo<-")
exportMethods("dictRef<-")
exportMethods("dict_location<-")
exportMethods("dictionary<-")
exportMethods("entities<-")
exportMethods("groupConfig<-")
exportMethods("groupwiseConfigRef<-")
exportMethods("icConfig<-")
exportMethods("ontology<-")
exportMethods("pairwiseConfig<-")
exportMethods("pairwiseConfigRef<-")
exportMethods("paramValueIndex<-")
exportMethods("scores<-")
exportMethods("simil<-")
exportMethods("similarityInstance<-")
exportMethods("typeSystemRef<-")
exportMethods(CaseMatch)
exportMethods(FindAllMatches)
exportMethods(OrderIndependentLookup)
exportMethods(SearchStrategy)
exportMethods(Stemmer)
exportMethods(StopWords)
exportMethods(SynonymType)
exportMethods(annotate)
exportMethods(annotateDF)
exportMethods(collapse)
exportMethods(compare)
exportMethods(dictInfo)
exportMethods(dictRef)
exportMethods(dict_location)
exportMethods(dictionary)
exportMethods(entities)
exportMethods(filterconcepts)
exportMethods(findEntities)
exportMethods(groupConfig)
exportMethods(groupsim)
exportMethods(groupwiseConfigRef)
exportMethods(icConfig)
exportMethods(mergeonassis)
exportMethods(multisim)
exportMethods(ontology)
exportMethods(pairsim)
exportMethods(pairwiseConfig)
exportMethods(pairwiseConfigRef)
exportMethods(paramValueIndex)
exportMethods(samplesim)
exportMethods(scores)
exportMethods(sim)
exportMethods(simil)
exportMethods(similarityInstance)
exportMethods(typeSystemRef)
import(OnassisJavaLibs)
import(data.table)
importFrom(AnnotationDbi,toTable)
importFrom(GEOmetadb,getSQLiteFile)
importFrom(RCurl,url.exists)
importFrom(RSQLite,SQLite)
importFrom(RSQLite,dbConnect)
importFrom(RSQLite,dbGetQuery)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(rJava,.jarray)
importFrom(rJava,.jcall)
importFrom(rJava,.jcast)
importFrom(rJava,.jevalArray)
importFrom(rJava,.jfield)
importFrom(rJava,.jinit)
importFrom(rJava,.jnew)
importFrom(rJava,.jnull)
importFrom(rJava,.jpackage)
importFrom(rJava,J)
importFrom(rJava,is.jnull)
importFrom(tools,file_ext)
importFrom(utils,download.file)
importFrom(utils,read.table)
importFrom(utils,tail)
