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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method("$",multiEnrichResult)
S3method("$",multiGseaResult)
S3method("+",EMP)
S3method("+",EMPT)
S3method("[",multiEnrichResult)
S3method("[",multiGseaResult)
S3method("[[",multiEnrichResult)
S3method("[[",multiGseaResult)
S3method(as.data.frame,multiEnrichResult)
S3method(as.data.frame,multiGseaResult)
S3method(dim,multiEnrichResult)
S3method(dim,multiGseaResult)
S3method(geneID,multiEnrichResult)
S3method(geneID,multiGseaResult)
S3method(geneInCategory,multiEnrichResult)
S3method(geneInCategory,multiGseaResult)
S3method(head,multiEnrichResult)
S3method(head,multiGseaResult)
S3method(tail,multiEnrichResult)
S3method(tail,multiGseaResult)
export("EMP_result<-")
export(EMP_GSEA_analysis)
export(EMP_GSEA_plot)
export(EMP_WGCNA_cluster_analysis)
export(EMP_WGCNA_cor_analysis)
export(EMP_adjust_abundance)
export(EMP_alpha_analysis)
export(EMP_assay_extract)
export(EMP_boxplot)
export(EMP_cluster_analysis)
export(EMP_coldata_extract)
export(EMP_collapse)
export(EMP_cor_analysis)
export(EMP_decostand)
export(EMP_diff_analysis)
export(EMP_dimension_analysis)
export(EMP_easy_import)
export(EMP_enrich_analysis)
export(EMP_enrich_dotplot)
export(EMP_enrich_netplot)
export(EMP_feature_convert)
export(EMP_filter)
export(EMP_fitline_plot)
export(EMP_function_import)
export(EMP_heatmap_plot)
export(EMP_history)
export(EMP_identify_assay)
export(EMP_impute)
export(EMP_marker_analysis)
export(EMP_message)
export(EMP_modify_assay)
export(EMP_multi_analysis)
export(EMP_network_analysis)
export(EMP_network_plot)
export(EMP_normal_import)
export(EMP_result)
export(EMP_rowdata_extract)
export(EMP_rrarefy)
export(EMP_sankey_plot)
export(EMP_save_var)
export(EMP_scatterplot)
export(EMP_structure_plot)
export(EMP_summary)
export(EMP_taxonomy_import)
export(EMP_to_EMP1)
export(EMP_volcanol_plot)
export(NetEnrich)
export(NetEnrich_rank)
export(NetPEA)
export(NetPEA2)
export(RWR)
export(build_gson)
export(cmi)
export(geneID)
export(geneInCategory)
export(get_Xd)
export(get_Xd2)
export(list2dataframe)
export(multiEnrichResult2enrichResult)
export(multiEnrichment)
export(multiNetEnrich)
export(r)
export(str_detect_multi)
export(top_detect)
export(wide2long)
export(wide2long_spMatrix)
exportClasses(EMP)
exportClasses(EMPT)
exportClasses(multiEnrichResult)
exportClasses(multiGseaResult)
exportMethods(EMP_GSEA_plot)
exportMethods(EMP_enrich_dotplot)
exportMethods(EMP_enrich_netplot)
exportMethods(EMP_scatterplot)
import(dynamicTreeCut)
import(ggplot2)
import(ggthemes)
importFrom(BiocManager,install)
importFrom(Boruta,Boruta)
importFrom(DOSE,enrichDO)
importFrom(DOSE,gseDO)
importFrom(Matrix,Matrix)
importFrom(Matrix,spMatrix)
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(MultiAssayExperiment,experiments)
importFrom(S4Vectors,DataFrame)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,`assayNames<-`)
importFrom(SummarizedExperiment,`colData<-`)
importFrom(SummarizedExperiment,`rowData<-`)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(WGCNA,labels2colors)
importFrom(WGCNA,orderMEs)
importFrom(aplot,insert_left)
importFrom(aplot,insert_top)
importFrom(bigstatsr,big_SVD)
importFrom(biomformat,biom)
importFrom(biomformat,biom_data)
importFrom(biomformat,observation_metadata)
importFrom(biomformat,read_hdf5_biom)
importFrom(bootnet,estimateNetwork)
importFrom(clusterProfiler,GSEA)
importFrom(clusterProfiler,compareCluster)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,enrichWP)
importFrom(clusterProfiler,enricher)
importFrom(clusterProfiler,gseGO)
importFrom(clusterProfiler,gson_KEGG)
importFrom(clusterProfiler,merge_result)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,contains)
importFrom(dplyr,desc)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,last_col)
importFrom(dplyr,matches)
importFrom(dplyr,mutate)
importFrom(dplyr,n_distinct)
importFrom(dplyr,ntile)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,where)
importFrom(enrichplot,cnetplot)
importFrom(enrichplot,dotplot)
importFrom(enrichplot,gseaplot2)
importFrom(fastcluster,hclust)
importFrom(forcats,fct_relevel)
importFrom(ggiraph,geom_jitter_interactive)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,theme_minimal)
importFrom(ggrepel,geom_text_repel)
importFrom(ggsignif,geom_signif)
importFrom(ggtree,ggtree)
importFrom(glue,glue_collapse)
importFrom(graphics,abline)
importFrom(gson,gson)
importFrom(impute,impute.knn)
importFrom(infotheo,entropy)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(memoise,forget)
importFrom(memoise,memoise)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(missRanger,missRanger)
importFrom(networkD3,sankeyNetwork)
importFrom(parallel,detectCores)
importFrom(patchwork,plot_layout)
importFrom(pillar,tbl_format_footer)
importFrom(pillar,tbl_format_header)
importFrom(pillar,tbl_format_setup)
importFrom(psych,corr.test)
importFrom(purrr,reduce)
importFrom(qgraph,centralityPlot)
importFrom(qgraph,centralityTable)
importFrom(qvalue,qvalue)
importFrom(randomForest,randomForest)
importFrom(rlang,`:=`)
importFrom(rlang,new_formula)
importFrom(snowfall,sfLapply)
importFrom(snowfall,sfStop)
importFrom(spsUtil,quiet)
importFrom(stats,aov)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,ave)
importFrom(stats,cmdscale)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_match)
importFrom(stringr,str_replace_all)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidybulk,adjust_abundance)
importFrom(tidybulk,tidybulk)
importFrom(tidyr,drop_na)
importFrom(tidyr,pivot_wider)
importFrom(utils,combn)
importFrom(utils,getFromNamespace)
importFrom(utils,head)
importFrom(utils,install.packages)
importFrom(utils,menu)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,unzip)
importFrom(vegan,adonis2)
importFrom(vegan,decostand)
importFrom(vegan,diversity)
importFrom(vegan,vegdist)
importFrom(withr,with_seed)
importFrom(xgboost,xgb.DMatrix)
importFrom(xgboost,xgb.importance)
importFrom(xgboost,xgboost)
importFrom(yulab.utils,yread)