NAMESPACE

# Generated by roxygen2: do not edit by hand

export(IQR.filter)
export(NetBID.analysis.dir.create)
export(NetBID.lazyMode.DriverEstimation)
export(NetBID.lazyMode.DriverVisualization)
export(NetBID.loadRData)
export(NetBID.network.dir.create)
export(NetBID.saveRData)
export(RNASeqCount.normalize.scale)
export(SJAracne.prepare)
export(bid)
export(cal.Activity)
export(cal.Activity.GS)
export(combineDE)
export(combinePvalVector)
export(db.preload)
export(draw.2D)
export(draw.2D.ellipse)
export(draw.2D.interactive)
export(draw.2D.text)
export(draw.3D)
export(draw.GSEA)
export(draw.GSEA.NetBID)
export(draw.GSEA.NetBID.GS)
export(draw.MICA)
export(draw.NetBID)
export(draw.bubblePlot)
export(draw.categoryValue)
export(draw.clustComp)
export(draw.combineDE)
export(draw.emb.kmeans)
export(draw.eset.QC)
export(draw.funcEnrich.bar)
export(draw.funcEnrich.cluster)
export(draw.heatmap)
export(draw.network.QC)
export(draw.oncoprint)
export(draw.targetNet)
export(draw.targetNet.TWO)
export(draw.volcanoPlot)
export(funcEnrich.Fisher)
export(funcEnrich.GSEA)
export(generate.eset)
export(generate.masterTable)
export(get.SJAracne.network)
export(get.TF_SIG.list)
export(get.class.color)
export(getDE.BID.2G)
export(getDE.limma.2G)
export(get_IDtransfer)
export(get_IDtransfer2symbol2type)
export(get_IDtransfer_betweenSpecies)
export(get_clustComp)
export(get_int_group)
export(get_name_transfertab)
export(get_net2target_list)
export(get_obs_label)
export(gs.preload)
export(load.exp.GEO)
export(load.exp.RNASeq.demo)
export(load.exp.RNASeq.demoSalmon)
export(merge_TF_SIG.AC)
export(merge_TF_SIG.network)
export(merge_eset)
export(merge_gs)
export(merge_target_list)
export(out2excel)
export(processDriverProfile)
export(test.targetNet.overlap)
export(update_SJAracne.network)
export(update_eset.feature)
export(update_eset.phenotype)
export(z2col)
import(Biobase)
import(ConsensusClusterPlus)
import(biomaRt)
import(igraph)
import(kableExtra)
import(limma)
import(msigdbr)
import(openxlsx)
import(tximport)
importFrom(ComplexHeatmap,Heatmap)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromTximport)
importFrom(GEOquery,getGEO)
importFrom(GSVA,gsva)
importFrom(MCMCglmm,MCMCglmm)
importFrom(Matrix,rowSums)
importFrom(RColorBrewer,brewer.pal)
importFrom(SummarizedExperiment,assay)
importFrom(aricode,clustComp)
importFrom(arm,bayesglm)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,segments)
importFrom(graphics,strheight)
importFrom(graphics,stripchart)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(impute,impute.knn)
importFrom(lme4,lmer)
importFrom(ordinal,clm)
importFrom(ordinal,clmm)
importFrom(plot3D,scatter3D)
importFrom(plotrix,draw.circle)
importFrom(plotrix,draw.ellipse)
importFrom(reshape,melt)
importFrom(rhdf5,H5Fclose)
importFrom(rhdf5,H5Fopen)
importFrom(rmarkdown,html_document)
importFrom(rmarkdown,pandoc_available)
importFrom(rmarkdown,render)
importFrom(stats,IQR)
importFrom(stats,aggregate)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,cutree)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,gaussian)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,ks.test)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pnorm)
importFrom(stats,prcomp)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,splinefun)
importFrom(umap,umap)
importFrom(umap,umap.defaults)
importFrom(utils,read.delim)
importFrom(utils,write.table)