# Generated by roxygen2: do not edit by hand

S3method(add,default)
S3method(estimateLogicle,GatingHierarchy)
S3method(filterObject,default)
S3method(filter_to_list,booleanFilter)
S3method(filter_to_list,ellipsoidGate)
S3method(filter_to_list,logical)
S3method(filter_to_list,polygonGate)
S3method(filter_to_list,quadGate)
S3method(filter_to_list,rectangleGate)
S3method(getCompensationMatrices,GatingHierarchy)
S3method(getStats,GatingHierarchy)
S3method(getStats,GatingSet)
S3method(getStats,GatingSetList)
S3method(getTransformations,GatingHierarchy)
S3method(pop_add,factor)
S3method(pop_add,filter)
S3method(pop_add,filters)
S3method(pop_add,logical)
S3method(pop_add,logicalFilterResult)
S3method(pop_add,multipleFilterResult)
S3method(pop_add,quadGate)
S3method(realize_view,cytoframe)
S3method(realize_view,cytoset)
S3method(recompute,GatingSet)
S3method(recompute,GatingSetList)
S3method(rotate_gate,GatingHierarchy)
S3method(rotate_gate,GatingSet)
S3method(scale_gate,GatingHierarchy)
S3method(scale_gate,GatingSet)
S3method(shift_gate,GatingHierarchy)
S3method(shift_gate,GatingSet)
S3method(subset,GatingSet)
S3method(subset,cytoset)
S3method(transform_gate,GatingHierarchy)
S3method(transform_gate,GatingSet)
export("flowData<-")
export("gs_cyto_data<-")
export(.getNodeInd)
export(GatingSetList)
export(Rm)
export(add)
export(asinh_Gml2)
export(asinhtGml2_trans)
export(booleanFilter)
export(cf_append_cols)
export(cf_cleanup)
export(cf_cleanup_temp)
export(cf_flush_meta)
export(cf_get_h5_file_path)
export(cf_get_uri)
export(cf_is_subsetted)
export(cf_keyword_delete)
export(cf_keyword_insert)
export(cf_keyword_rename)
export(cf_keyword_set)
export(cf_load_meta)
export(cf_lock)
export(cf_rename_channel)
export(cf_rename_marker)
export(cf_swap_colnames)
export(cf_unlock)
export(cf_write_disk)
export(cf_write_h5)
export(cf_write_tile)
export(char2booleanFilter)
export(checkRedundantNodes)
export(convert_backend)
export(convert_legacy_gs)
export(convert_legacy_gslist)
export(copyNode)
export(cs_add_cytoframe)
export(cs_cleanup_temp)
export(cs_flush_meta)
export(cs_get_cytoframe)
export(cs_get_h5_file_path)
export(cs_get_uri)
export(cs_is_subsetted)
export(cs_keyword_delete)
export(cs_keyword_insert)
export(cs_keyword_rename)
export(cs_keyword_set)
export(cs_load_meta)
export(cs_lock)
export(cs_set_cytoframe)
export(cs_swap_colnames)
export(cs_unlock)
export(ctx_to_list)
export(cytoctx)
export(cytoframe_to_flowFrame)
export(cytoset)
export(cytoset_to_flowSet)
export(cytoset_to_list)
export(delete_gs)
export(dropRedundantChannels)
export(dropRedundantNodes)
export(extract_cluster_pop_name_from_node)
export(filterObject)
export(filter_to_list)
export(flowData)
export(flowFrame_to_cytoframe)
export(flowJo.fasinh)
export(flowJo.flog)
export(flowJo.fsinh)
export(flowJoTrans)
export(flowJo_biexp_trans)
export(flowJo_fasinh_trans)
export(flowSet_to_cytoset)
export(flow_breaks)
export(flow_trans)
export(flowjo_biexp)
export(flowjo_biexp_trans)
export(flowjo_fasinh)
export(flowjo_fasinh_trans)
export(flowjo_fsinh)
export(flowjo_log_trans)
export(getChildren)
export(getCompensationMatrices)
export(getData)
export(getDescendants)
export(getGate)
export(getNodes)
export(getParent)
export(getPopStats)
export(getProp)
export(getSingleCellExpression)
export(getSingleCellExpressionByGate)
export(getStats)
export(getTotal)
export(getTransformations)
export(get_cytoframe_from_cs)
export(get_default_backend)
export(get_leaf_nodes)
export(get_log_level)
export(gh_apply_to_cs)
export(gh_apply_to_new_fcs)
export(gh_cleanup_temp)
export(gh_copy_gate)
export(gh_get_cluster_labels)
export(gh_get_compensations)
export(gh_get_leaf_nodes)
export(gh_get_pop_paths)
export(gh_get_transformations)
export(gh_keyword_delete)
export(gh_keyword_insert)
export(gh_keyword_rename)
export(gh_keyword_set)
export(gh_plot_pop_count_cv)
export(gh_pop_compare_stats)
export(gh_pop_get_children)
export(gh_pop_get_cluster_name)
export(gh_pop_get_count)
export(gh_pop_get_data)
export(gh_pop_get_descendants)
export(gh_pop_get_full_path)
export(gh_pop_get_gate)
export(gh_pop_get_indices)
export(gh_pop_get_indices_mat)
export(gh_pop_get_parent)
export(gh_pop_get_proportion)
export(gh_pop_get_stats)
export(gh_pop_get_stats_tfilter)
export(gh_pop_is_bool_gate)
export(gh_pop_is_gated)
export(gh_pop_is_hidden)
export(gh_pop_is_negated)
export(gh_pop_move)
export(gh_pop_remove)
export(gh_pop_set_gate)
export(gh_pop_set_indices)
export(gh_pop_set_name)
export(gh_pop_set_visibility)
export(gh_pop_set_xml_count)
export(groupByChannels)
export(groupByTree)
export(gs_check_redundant_nodes)
export(gs_cleanup_temp)
export(gs_clone)
export(gs_copy_tree_only)
export(gs_cyto_data)
export(gs_get_compensation_internal)
export(gs_get_compensations)
export(gs_get_cytoframe)
export(gs_get_leaf_nodes)
export(gs_get_pop_paths)
export(gs_get_singlecell_expression)
export(gs_get_singlecell_expression_by_gate)
export(gs_get_uri)
export(gs_is_h5)
export(gs_is_persistent)
export(gs_keyword_delete)
export(gs_keyword_insert)
export(gs_keyword_rename)
export(gs_keyword_set)
export(gs_plot_diff_tree)
export(gs_plot_pop_count_cv)
export(gs_pop_add)
export(gs_pop_get_children)
export(gs_pop_get_count_fast)
export(gs_pop_get_count_with_meta)
export(gs_pop_get_data)
export(gs_pop_get_gate)
export(gs_pop_get_gs)
export(gs_pop_get_parent)
export(gs_pop_get_stats)
export(gs_pop_get_stats_tfilter)
export(gs_pop_remove)
export(gs_pop_set_gate)
export(gs_pop_set_name)
export(gs_pop_set_visibility)
export(gs_remove_redundant_channels)
export(gs_remove_redundant_nodes)
export(gs_split_by_channels)
export(gs_split_by_tree)
export(gs_update_channels)
export(gslist_to_gs)
export(isGated)
export(isHidden)
export(isNcdf)
export(isNegated)
export(is_tiledb_support)
export(load_cytoframe)
export(load_cytoframe_from_fcs)
export(load_cytoset)
export(load_cytoset_from_fcs)
export(load_gs)
export(load_gslist)
export(logicleGml2_trans)
export(logicle_trans)
export(logtGml2_trans)
export(merge_list_to_gs)
export(moveNode)
export(openWorkspace)
export(plotGate)
export(pop.MFI)
export(pop_add)
export(prettyAxis)
export(print.cytoctx)
export(realize_view)
export(recompute)
export(save_cytoset)
export(save_gs)
export(save_gslist)
export(setGate)
export(setNode)
export(set_default_backend)
export(set_log_level)
export(swap_data_cols)
export(transformerList)
export(updateChannels)
exportClasses(GatingHierarchy)
exportClasses(GatingSet)
exportClasses(GatingSetList)
exportClasses(booleanFilter)
exportClasses(cytoframe)
exportClasses(cytoset)
exportMethods("[")
exportMethods("[[")
exportMethods("[[<-")
exportMethods("colnames<-")
exportMethods("flowData<-")
exportMethods("gs_cyto_data<-")
exportMethods("identifier<-")
exportMethods("markernames<-")
exportMethods("pData<-")
exportMethods("phenoData<-")
exportMethods("rownames<-")
exportMethods("sampleNames<-")
exportMethods(GatingSet)
exportMethods(colnames)
exportMethods(compensate)
exportMethods(dimnames)
exportMethods(flowData)
exportMethods(getChildren)
exportMethods(getData)
exportMethods(getGate)
exportMethods(getIndices)
exportMethods(getNodes)
exportMethods(getParent)
exportMethods(getPopStats)
exportMethods(gs_cyto_data)
exportMethods(identifier)
exportMethods(keyword)
exportMethods(lapply)
exportMethods(length)
exportMethods(markernames)
exportMethods(pData)
exportMethods(phenoData)
exportMethods(plot)
exportMethods(rbind2)
exportMethods(rownames)
exportMethods(sampleNames)
exportMethods(setGate)
exportMethods(setNode)
exportMethods(show)
exportMethods(transform)
exportMethods(updateIndices)
import(data.table)
import(flowCore)
import(ncdfFlow)
importClassesFrom(XML,XMLInternalDocument)
importClassesFrom(flowCore,flowFrame)
importClassesFrom(flowCore,flowSet)
importClassesFrom(graph,graphNEL)
importClassesFrom(methods,ANY)
importClassesFrom(methods,character)
importClassesFrom(methods,data.frame)
importClassesFrom(methods,environment)
importClassesFrom(methods,list)
importClassesFrom(methods,logical)
importClassesFrom(methods,matrix)
importClassesFrom(methods,missing)
importClassesFrom(methods,numeric)
importClassesFrom(methods,oldClass)
importFrom(Biobase,"pData<-")
importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,description)
importFrom(Biobase,exprs)
importFrom(Biobase,pData)
importFrom(Biobase,read.AnnotatedDataFrame)
importFrom(Biobase,sampleNames)
importFrom(BiocGenerics,"rownames<-")
importFrom(BiocGenerics,duplicated)
importFrom(BiocGenerics,rownames)
importFrom(Rcpp,evalCpp)
importFrom(RcppParallel,RcppParallelLibs)
importFrom(Rgraphviz,agread)
importFrom(S4Vectors,coolcat)
importFrom(aws.s3,delete_object)
importFrom(aws.s3,get_bucket)
importFrom(aws.s3,get_bucket_df)
importFrom(aws.s3,put_object)
importFrom(aws.s3,save_object)
importFrom(aws.signature,read_credentials)
importFrom(cytolib,cytolib_LdFlags)
importFrom(digest,digest)
importFrom(dplyr,"%>%")
importFrom(dplyr,bind_rows)
importFrom(dplyr,do)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(flowCore,collapse_desc)
importFrom(flowCore,identifier)
importFrom(graph,"edgeRenderInfo<-")
importFrom(graph,"nodeRenderInfo<-")
importFrom(graph,addEdge)
importFrom(graph,graphNEL)
importFrom(lattice,barchart)
importFrom(latticeExtra,ggplot2like)
importFrom(matrixStats,colMedians)
importFrom(scales,format_format)
importFrom(scales,trans_new)
importFrom(stats4,plot)
importMethodsFrom(Biobase,"sampleNames<-")
importMethodsFrom(Rgraphviz,AgEdge)
importMethodsFrom(Rgraphviz,AgNode)
importMethodsFrom(Rgraphviz,name)
importMethodsFrom(Rgraphviz,nodeData)
importMethodsFrom(Rgraphviz,nodeDataDefaults)
importMethodsFrom(Rgraphviz,renderGraph)
importMethodsFrom(graph,"edgeData<-")
importMethodsFrom(graph,"edgeDataDefaults<-")
importMethodsFrom(graph,"nodeData<-")
importMethodsFrom(graph,"nodeDataDefaults<-")
importMethodsFrom(graph,addEdge)
importMethodsFrom(graph,addNode)
importMethodsFrom(graph,edgeData)
importMethodsFrom(graph,edges)
importMethodsFrom(graph,inEdges)
importMethodsFrom(graph,nodeData)
importMethodsFrom(graph,nodes)
importMethodsFrom(graph,removeNode)
importMethodsFrom(graph,subGraph)
importMethodsFrom(methods,coerce)
importMethodsFrom(methods,show)
useDynLib(flowWorkspace,.registration = TRUE)
