NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(ggplot_add,geom_sc_wordcloud)
export(DimPlotWithTexts)
export(TextMarkers)
export(TextMarkersScran)
export(alliance)
export(biotextgraph)
export(bugsigdb)
export(changeLayout)
export(compareWordNet)
export(connectGenes)
export(convertMetaCyc)
export(enzyme)
export(exportCyjs)
export(exportCyjsWithoutImage)
export(exportVisjs)
export(exportWCNetwork)
export(findTerm)
export(geom_node_shadowtext)
export(geom_sc_wordcloud)
export(getSlot)
export(getUPtax)
export(getWordsOnDendro)
export(ggplot_add.geom_sc_wordcloud)
export(graph_cluster)
export(makeBar)
export(make_TDM)
export(make_corpus)
export(make_graph)
export(manual)
export(obtainMarkersWC)
export(obtainMarkersWCScran)
export(obtainTextPosition)
export(obtain_alliance)
export(obtain_bugsigdb)
export(obtain_enrich)
export(obtain_enzyme)
export(obtain_manual)
export(obtain_pubmed)
export(obtain_refseq)
export(parseMetaCycPathway)
export(perform_ora)
export(plotDynamic)
export(plotEigengeneNetworksWithWords)
export(plotNet)
export(plotORA)
export(plotReducedDimWithTexts)
export(plotWC)
export(plot_biofabric)
export(plot_biotextgraph)
export(plot_wordcloud)
export(process_network_gene)
export(process_network_manual)
export(process_network_microbe)
export(pubmed)
export(refseq)
export(refseqDESeq2)
export(refseqWGCNA)
export(returnExample)
export(returnSim)
export(set_filter_words)
export(tag_words)
export(textORA)
exportMethods(getSlot)
import(GeneSummary)
import(bugsigdbr)
import(ggplot2)
import(ggraph)
import(grid)
import(gridExtra)
import(igraph)
import(jsonlite)
import(methods)
import(org.Hs.eg.db)
import(patchwork)
import(rentrez)
import(tm)
import(wordcloud)
importFrom(AnnotationDbi,keys)
importFrom(GeneSummary,loadGeneSummary)
importFrom(GetoptLong,qqcat)
importFrom(MASS,cov.trob)
importFrom(NLP,ngrams)
importFrom(NLP,words)
importFrom(RColorBrewer,brewer.pal)
importFrom(XML,xmlElementsByTagName)
importFrom(XML,xmlParse)
importFrom(XML,xmlTreeParse)
importFrom(XML,xmlValue)
importFrom(XML,xpathSApply)
importFrom(cowplot,as_grob)
importFrom(cyjShiny,dataFramesToJSON)
importFrom(data.table,fread)
importFrom(dendextend,as.ggdend)
importFrom(dendextend,get_nodes_attr)
importFrom(dendextend,get_subdendrograms)
importFrom(dendextend,hang.dendrogram)
importFrom(dendextend,nnodes)
importFrom(dendextend,pvclust_show_signif_gradient)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,if_else)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(ggdendro,dendro_data)
importFrom(ggdendro,label)
importFrom(ggforce,geom_mark_hull)
importFrom(ggplot2,ggplot_add)
importFrom(ggplotify,as.ggplot)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,palette)
importFrom(graphlayouts,layout_as_dynamic)
importFrom(igraph,graph.adjacency)
importFrom(igraph,graph_from_edgelist)
importFrom(pvclust,pvclust)
importFrom(pvclust,pvpick)
importFrom(shadowtext,GeomShadowText)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,dhyper)
importFrom(stats,dist)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,reorder)
importFrom(tidygraph,activate)
importFrom(tidygraph,as_tbl_graph)
importFrom(tidygraph,graph_join)
importFrom(tidygraph,is.tbl_graph)
importFrom(tidygraph,tbl_graph)
importFrom(utils,object.size)