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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method("$",CondaEnv)
S3method("$",CondaEnvManager)
S3method("$",CondaEnvSlot)
S3method("$<-",CondaEnvManager)
S3method("$<-",CondaEnvSlot)
S3method("[",CondaEnvManager)
S3method("[<-",CondaEnvManager)
S3method("[[",CondaEnv)
S3method("[[",CondaEnvManager)
S3method("[[",CondaEnvSlot)
S3method("[[<-",CondaEnvManager)
S3method(.DollarNames,CondaEnv)
S3method(.DollarNames,CondaEnvManager)
S3method(.DollarNames,CondaEnvSlot)
S3method(as.data.frame,CondaEnv)
S3method(as.data.frame,CondaEnvManager)
S3method(as.data.frame,CondaEnvSlot)
S3method(as.list,CondaEnv)
S3method(as.list,CondaEnvManager)
S3method(as.list,CondaEnvSlot)
S3method(ggplot2::ggplot_add,fullsizebar)
S3method(stats::median,numeric_lisi)
S3method(vctrs::vec_cast,numeric_lisi)
S3method(vctrs::vec_ptype2,numeric_lisi)
S3method(vec_cast.numeric_lisi,numeric_lisi)
S3method(vec_ptype2.numeric_lisi,double)
S3method(vec_ptype2.numeric_lisi,numeric)
S3method(vec_ptype2.numeric_lisi,numeric_lisi)
export(AddScoreARI)
export(AddScoreASW)
export(AddScoreASWBatch)
export(AddScoreConnectivity)
export(AddScoreDensityPC)
export(AddScoreKBET)
export(AddScoreLISI)
export(AddScoreNMI)
export(AddScoreRegressPC)
export(AddScoreRegressPC.CellCycle)
export(CellCycleScoringPerBatch)
export(CombatIntegration)
export(CondaEnv)
export(CondaManager)
export(CutKnn)
export(DoIntegrate)
export(ExpandNeighbours)
export(FindOptimalClusters)
export(GetConnectivities)
export(GetMiscIntegrations)
export(GetMiscScores)
export(GetNeighborsPerBatch)
export(GetPropInterBatch)
export(GetPropIntraBatch)
export(HarmonyIntegration)
export(HarmonyIntegration.fix)
export(IntegrationScores)
export(MNNIntegration)
export(NormaliseL2)
export(PlotScores)
export(ScaleScores)
export(ScanoramaIntegration)
export(ScoreARI)
export(ScoreASW)
export(ScoreASWBatch)
export(ScoreConnectivity)
export(ScoreDensityPC)
export(ScoreKBET)
export(ScoreLISI)
export(ScoreNMI)
export(ScoreRegressPC)
export(ScoreRegressPC.CellCycle)
export(SymmetrizeKnn)
export(UpdateEnvCache)
export(bbknnIntegration)
export(checkCondaBin)
export(checkCondaEnv)
export(checkCondaEnvName)
export(checkCondaEnvPath)
export(getCache)
export(getCachePath)
export(isValid)
export(reloadCache)
export(resetCache)
export(rowSort)
export(rowcol2idx)
export(saveToCache)
export(scANVIIntegration)
export(scVIIntegration)
export(scVIIntegration.fix)
export(symmetrize.pmax.sparse)
export(trVAEIntegration)
exportClasses(CondaEnv)
exportClasses(CondaEnvManager)
exportMethods(ExpandNeighbours)
exportMethods(SymmetrizeKnn)
exportMethods(isValid)
import(rlang)
importFrom(Matrix,"diag<-")
importFrom(Matrix,colSums)
importFrom(Matrix,diag)
importFrom(Matrix,drop0)
importFrom(Matrix,isSymmetric)
importFrom(Matrix,rowSums)
importFrom(Matrix,spMatrix)
importFrom(Matrix,sparse.model.matrix)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(RhpcBLASctl,blas_get_num_procs)
importFrom(RhpcBLASctl,blas_set_num_threads)
importFrom(RhpcBLASctl,omp_get_num_procs)
importFrom(RhpcBLASctl,omp_set_num_threads)
importFrom(Seurat,"DefaultAssay<-")
importFrom(Seurat,"Tool<-")
importFrom(Seurat,"VariableFeatures<-")
importFrom(Seurat,CellCycleScoring)
importFrom(Seurat,Cells)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,CreateDimReducObject)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,DefaultAssay)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,LogSeuratCommand)
importFrom(Seurat,RunPCA)
importFrom(Seurat,SelectIntegrationFeatures)
importFrom(Seurat,SelectIntegrationFeatures5)
importFrom(Seurat,SelectSCTIntegrationFeatures)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,as.SingleCellExperiment)
importFrom(SeuratObject,"%iff%")
importFrom(SeuratObject,"DefaultAssay<-")
importFrom(SeuratObject,"Misc<-")
importFrom(SeuratObject,AddMetaData)
importFrom(SeuratObject,Cells)
importFrom(SeuratObject,CheckDots)
importFrom(SeuratObject,CreateAssayObject)
importFrom(SeuratObject,CreateDimReducObject)
importFrom(SeuratObject,DefaultAssay)
importFrom(SeuratObject,DefaultDimReduc)
importFrom(SeuratObject,Embeddings)
importFrom(SeuratObject,EmptyDF)
importFrom(SeuratObject,Features)
importFrom(SeuratObject,GetAssayData)
importFrom(SeuratObject,Graphs)
importFrom(SeuratObject,JoinLayers)
importFrom(SeuratObject,LayerData)
importFrom(SeuratObject,Layers)
importFrom(SeuratObject,LogSeuratCommand)
importFrom(SeuratObject,Misc)
importFrom(SeuratObject,Neighbors)
importFrom(SeuratObject,Reductions)
importFrom(SeuratObject,SetAssayData)
importFrom(SeuratObject,VariableFeatures)
importFrom(SeuratObject,as.Graph)
importFrom(SeuratObject,as.Neighbor)
importFrom(SummarizedExperiment,assay)
importFrom(batchelor,mnnCorrect)
importFrom(broom,glance)
importFrom(cli,ansi_align)
importFrom(cli,ansi_nchar)
importFrom(cli,bg_blue)
importFrom(cli,col_blue)
importFrom(cli,col_br_white)
importFrom(cli,col_green)
importFrom(cli,col_grey)
importFrom(cli,col_red)
importFrom(cli,rule)
importFrom(cli,style_bold)
importFrom(cli,style_dim)
importFrom(cli,style_strikethrough)
importFrom(cli,symbol)
importFrom(cluster,silhouette)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,"%>%")
importFrom(dplyr,`%>%`)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,c_across)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,cur_column)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_map)
importFrom(dplyr,group_modify)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pick)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(dplyr,where)
importFrom(forcats,fct_relabel)
importFrom(forcats,fct_reorder)
importFrom(forcats,fct_rev)
importFrom(future,"%<-%")
importFrom(future,"%packages%")
importFrom(future,"%seed%")
importFrom(future,multicore)
importFrom(future,multisession)
importFrom(future,plan)
importFrom(future,sequential)
importFrom(ggplot2,CoordRadial)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_errorbarh)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,ggplot_add)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,guides)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_colour_distiller)
importFrom(ggplot2,scale_fill_distiller)
importFrom(ggplot2,scale_size_area)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,xlab)
importFrom(grid,unit)
importFrom(grid,unitType)
importFrom(harmony,RunHarmony)
importFrom(harmony,harmony_options)
importFrom(igraph,components)
importFrom(igraph,distances)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)
importFrom(parallel,mcmapply)
importFrom(parallelly,supportsMulticore)
importFrom(purrr,imap)
importFrom(purrr,map2)
importFrom(purrr,reduce)
importFrom(reticulate,conda_binary)
importFrom(reticulate,conda_create)
importFrom(reticulate,conda_install)
importFrom(reticulate,conda_list)
importFrom(reticulate,conda_remove)
importFrom(reticulate,condaenv_exists)
importFrom(reticulate,import)
importFrom(reticulate,import_builtins)
importFrom(reticulate,py_to_r)
importFrom(reticulate,r_to_py)
importFrom(reticulate,use_condaenv)
importFrom(rlang,"!!!")
importFrom(rlang,"!!")
importFrom(rlang,"%||%")
importFrom(rlang,":=")
importFrom(rlang,abort)
importFrom(rlang,arg_match)
importFrom(rlang,as_label)
importFrom(rlang,call2)
importFrom(rlang,call_args)
importFrom(rlang,call_match)
importFrom(rlang,call_modify)
importFrom(rlang,call_name)
importFrom(rlang,call_ns)
importFrom(rlang,check_installed)
importFrom(rlang,data_sym)
importFrom(rlang,data_syms)
importFrom(rlang,enquos)
importFrom(rlang,eval_tidy)
importFrom(rlang,fn_fmls_names)
importFrom(rlang,is_installed)
importFrom(rlang,maybe_missing)
importFrom(rlang,quo)
importFrom(rlang,quo_get_expr)
importFrom(rlang,quo_set_expr)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(scales,rescale)
importFrom(stats,as.formula)
importFrom(stats,bw.SJ)
importFrom(stats,bw.bcv)
importFrom(stats,bw.nrd)
importFrom(stats,bw.nrd0)
importFrom(stats,bw.ucv)
importFrom(stats,density)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,summary.lm)
importFrom(stats,xtabs)
importFrom(sva,ComBat)
importFrom(sva,ComBat_seq)
importFrom(tibble,add_column)
importFrom(tibble,add_row)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_longer)
importFrom(tools,R_user_dir)
importFrom(utils,.DollarNames)
importFrom(utils,adist)
importFrom(utils,capture.output)
importFrom(utils,getS3method)
importFrom(utils,globalVariables)
importFrom(utils,object.size)
importFrom(utils,setTxtProgressBar)
importFrom(vctrs,vec_cast)
importFrom(vctrs,vec_ptype2)