# Generated by roxygen2: do not edit by hand

S3method(cosine_sim,default)
S3method(cosine_sim,numeric)
S3method(jaccard_index,character)
S3method(jaccard_index,default)
S3method(overlap_coef,character)
S3method(overlap_coef,default)
S3method(tversky_index,character)
S3method(tversky_index,default)
S3method(vis,clonal_family)
S3method(vis,clonal_family_tree)
S3method(vis,immunr_chao1)
S3method(vis,immunr_clonal_prop)
S3method(vis,immunr_dbscan)
S3method(vis,immunr_div)
S3method(vis,immunr_dxx)
S3method(vis,immunr_dynamics)
S3method(vis,immunr_exp_clones)
S3method(vis,immunr_exp_count)
S3method(vis,immunr_exp_len)
S3method(vis,immunr_exp_vol)
S3method(vis,immunr_gene_usage)
S3method(vis,immunr_ginisimp)
S3method(vis,immunr_gu_matrix)
S3method(vis,immunr_hclust)
S3method(vis,immunr_hill)
S3method(vis,immunr_homeo)
S3method(vis,immunr_inc_overlap)
S3method(vis,immunr_invsimp)
S3method(vis,immunr_kmeans)
S3method(vis,immunr_kmer_profile_pfm)
S3method(vis,immunr_kmer_profile_ppm)
S3method(vis,immunr_kmer_profile_pwm)
S3method(vis,immunr_kmer_profile_self)
S3method(vis,immunr_kmer_table)
S3method(vis,immunr_mds)
S3method(vis,immunr_ov_matrix)
S3method(vis,immunr_pca)
S3method(vis,immunr_public_repertoire)
S3method(vis,immunr_public_statistics)
S3method(vis,immunr_rare_prop)
S3method(vis,immunr_rarefaction)
S3method(vis,immunr_spectr)
S3method(vis,immunr_spectr_nogene)
S3method(vis,immunr_top_prop)
S3method(vis,immunr_tsne)
S3method(vis,step_failure_ignored)
export(apply_asymm)
export(apply_symm)
export(bunch_translate)
export(coding)
export(cross_entropy)
export(dbAnnotate)
export(dbLoad)
export(entropy)
export(exclude)
export(fixVis)
export(geneUsage)
export(geneUsageAnalysis)
export(gene_stats)
export(getKmers)
export(get_genes)
export(immunr_dbscan)
export(immunr_hclust)
export(immunr_kmeans)
export(immunr_mds)
export(immunr_pca)
export(immunr_tsne)
export(inc_overlap)
export(include)
export(inframes)
export(interval)
export(js_div)
export(kl_div)
export(kmer_profile)
export(lessthan)
export(morethan)
export(noncoding)
export(outofframes)
export(pubRep)
export(pubRepApply)
export(pubRepFilter)
export(pubRepStatistics)
export(publicRepertoire)
export(publicRepertoireApply)
export(publicRepertoireFilter)
export(public_matrix)
export(repAlignLineage)
export(repClonalFamily)
export(repClonality)
export(repDiversity)
export(repExplore)
export(repFilter)
export(repGermline)
export(repLoad)
export(repOverlap)
export(repOverlapAnalysis)
export(repSample)
export(repSave)
export(repSomaticHypermutation)
export(select_barcodes)
export(select_clusters)
export(seqCluster)
export(seqDist)
export(spectratype)
export(split_to_kmers)
export(top)
export(trackClonotypes)
export(vis)
export(vis_bar)
export(vis_box)
export(vis_circos)
export(vis_heatmap)
export(vis_heatmap2)
export(vis_hist)
export(vis_immunr_kmer_profile_main)
export(vis_seqlogo)
export(vis_textlogo)
import(ggplot2)
importFrom(Rcpp,cppFunction)
importFrom(Rcpp,sourceCpp)
importFrom(UpSetR,fromExpression)
importFrom(UpSetR,upset)
importFrom(ape,as.DNAbin)
importFrom(ape,clustal)
importFrom(ape,read.tree)
importFrom(circlize,chordDiagram)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,melt.data.table)
importFrom(data.table,set)
importFrom(data.table,setDF)
importFrom(data.table,setDT)
importFrom(data.table,setcolorder)
importFrom(data.table,setnames)
importFrom(doParallel,registerDoParallel)
importFrom(doParallel,stopImplicitCluster)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,collect)
importFrom(dplyr,contains)
importFrom(dplyr,cur_group_id)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,first)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,group_keys)
importFrom(dplyr,group_map)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,one_of)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,select_)
importFrom(dplyr,select_if)
importFrom(dplyr,summarise)
importFrom(dplyr,tally)
importFrom(dplyr,top_n)
importFrom(dplyr,ungroup)
importFrom(dtplyr,lazy_dt)
importFrom(factoextra,fviz_cluster)
importFrom(factoextra,fviz_dend)
importFrom(factoextra,fviz_nbclust)
importFrom(factoextra,fviz_pca_ind)
importFrom(factoextra,hcut)
importFrom(fpc,dbscan)
importFrom(ggalluvial,geom_flow)
importFrom(ggalluvial,geom_stratum)
importFrom(ggpubr,compare_means)
importFrom(ggpubr,geom_signif)
importFrom(ggpubr,ggscatter)
importFrom(ggpubr,rotate_x_text)
importFrom(ggpubr,stat_compare_means)
importFrom(ggpubr,theme_pubr)
importFrom(ggraph,geom_edge_diagonal)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(ggraph,theme_graph)
importFrom(ggseqlogo,geom_logo)
importFrom(ggseqlogo,theme_logo)
importFrom(glue,glue)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,plot)
importFrom(grid,gpar)
importFrom(grid,rectGrob)
importFrom(igraph,clusters)
importFrom(igraph,graph_from_data_frame)
importFrom(jsonlite,read_json)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(magrittr,extract2)
importFrom(magrittr,set_attr)
importFrom(methods,as)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,parApply)
importFrom(parallel,stopCluster)
importFrom(patchwork,plot_annotation)
importFrom(patchwork,wrap_plots)
importFrom(phangorn,write.phyDat)
importFrom(pheatmap,pheatmap)
importFrom(plyr,.)
importFrom(plyr,adply)
importFrom(plyr,dlply)
importFrom(plyr,mapvalues)
importFrom(purrr,imap)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_chr)
importFrom(purrr,map2_df)
importFrom(purrr,map2_lgl)
importFrom(purrr,map_chr)
importFrom(purrr,map_df)
importFrom(purrr,map_dfr)
importFrom(purrr,map_lgl)
importFrom(purrr,pmap)
importFrom(readr,col_character)
importFrom(readr,col_double)
importFrom(readr,col_guess)
importFrom(readr,col_integer)
importFrom(readr,col_logical)
importFrom(readr,cols)
importFrom(readr,read_csv)
importFrom(readr,read_delim)
importFrom(readr,read_tsv)
importFrom(readr,write_lines)
importFrom(readxl,read_xlsx)
importFrom(reshape2,melt)
importFrom(rlang,sym)
importFrom(rlist,list.remove)
importFrom(scales,percent)
importFrom(shiny,actionButton)
importFrom(shiny,br)
importFrom(shiny,checkboxInput)
importFrom(shiny,downloadButton)
importFrom(shiny,downloadHandler)
importFrom(shiny,fluidPage)
importFrom(shiny,mainPanel)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,plotOutput)
importFrom(shiny,renderPlot)
importFrom(shiny,renderText)
importFrom(shiny,renderUI)
importFrom(shiny,selectInput)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,sliderInput)
importFrom(shiny,splitLayout)
importFrom(shiny,tabPanel)
importFrom(shiny,tabsetPanel)
importFrom(shiny,textAreaInput)
importFrom(shiny,textInput)
importFrom(shiny,textOutput)
importFrom(shiny,titlePanel)
importFrom(shiny,uiOutput)
importFrom(shiny,updateSliderInput)
importFrom(shinythemes,shinytheme)
importFrom(stats,as.dist)
importFrom(stats,cmdscale)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stats,qnorm)
importFrom(stats,rmultinom)
importFrom(stringdist,stringdistmatrix)
importFrom(stringi,stri_replace_all_fixed)
importFrom(stringr,boundary)
importFrom(stringr,fixed)
importFrom(stringr,str_c)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_length)
importFrom(stringr,str_match)
importFrom(stringr,str_order)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_sort)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(stringr,str_trim)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,drop_na)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyselect,all_of)
importFrom(tidyselect,any_of)
importFrom(tidyselect,starts_with)
importFrom(utils,capture.output)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
importFrom(uuid,UUIDgenerate)
useDynLib(immunarch, .registration = TRUE)
