# Generated by roxygen2: do not edit by hand

S3method(plot,GermlineCluster)
S3method(print,GermlineCluster)
S3method(summary,GermlineCluster)
export("%>%")
export(alleleClusterNames)
export(allele_diff)
export(allele_diff_indices)
export(allele_diff_indices_parallel)
export(allele_diff_indices_parallel2)
export(allele_diff_strings)
export(artificialFRW1Germline)
export(assignAlleleClusters)
export(detect_communities_leiden)
export(distance_to_graph)
export(extractASCTable)
export(germlineASC)
export(igClust)
export(igDistance)
export(ighvClust)
export(ighvDistance)
export(inferAlleleClusters)
export(inferGenotypeAllele)
export(inferGenotypeAllele_asc)
export(insert_gaps2_vec)
export(new_germline_cluster)
export(optimize_resolution)
export(plotClusterComparison)
export(plotCommunityNetwork)
export(plotSilhouetteOptimization)
export(plotTruncatedTree)
export(recentAlleleClusters)
export(zenodoArchive)
import(circlize)
import(dendextend)
import(ggplot2)
import(grDevices)
import(graphics)
import(jsonlite)
import(methods)
import(utils)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,unmasked)
importFrom(DECIPHER,DistanceMatrix)
importFrom(R6,R6Class)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(Rcpp,evalCpp)
importFrom(Rcpp,sourceCpp)
importFrom(alakazam,getAllele)
importFrom(alakazam,getFamily)
importFrom(alakazam,getGene)
importFrom(cluster,silhouette)
importFrom(data.table,"%chin%")
importFrom(data.table,":=")
importFrom(data.table,.N)
importFrom(data.table,.SD)
importFrom(data.table,CJ)
importFrom(data.table,data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,setDT)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(data.table,setorderv)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,cluster_leiden)
importFrom(igraph,cluster_louvain)
importFrom(igraph,edge_attr_names)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,is_igraph)
importFrom(igraph,membership)
importFrom(magrittr,"%>%")
importFrom(methods,setOldClass)
importFrom(rlang,.data)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,binom.test)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,setNames)
importFrom(stats,weighted.mean)
importFrom(stringdist,stringdistmatrix)
importFrom(tigger,findUnmutatedCalls)
importFrom(tigger,readIgFasta)
importFrom(zen4R,download_zenodo)
useDynLib(piglet, .registration = TRUE)
