# Generated by roxygen2: do not edit by hand

export(GDCdownload)
export(GDCprepare)
export(GDCprepare_clinic)
export(GDCquery)
export(GDCquery_Maf)
export(GDCquery_clinic)
export(PanCancerAtlas_subtypes)
export(TCGAVisualize_volcano)
export(TCGA_MolecularSubtype)
export(TCGAanalyze_Clustering)
export(TCGAanalyze_DEA)
export(TCGAanalyze_DEA_Affy)
export(TCGAanalyze_DMR)
export(TCGAanalyze_EAcomplete)
export(TCGAanalyze_Filtering)
export(TCGAanalyze_LevelTab)
export(TCGAanalyze_Normalization)
export(TCGAanalyze_Pathview)
export(TCGAanalyze_Preprocessing)
export(TCGAanalyze_SurvivalKM)
export(TCGAanalyze_analyseGRN)
export(TCGAanalyze_networkInference)
export(TCGAanalyze_survival)
export(TCGAbatch_Correction)
export(TCGAprepare_Affy)
export(TCGAquery_MatchedCoupledSampleTypes)
export(TCGAquery_SampleTypes)
export(TCGAquery_recount2)
export(TCGAquery_subtype)
export(TCGAtumor_purity)
export(TCGAvisualize_BarPlot)
export(TCGAvisualize_EAbarplot)
export(TCGAvisualize_Heatmap)
export(TCGAvisualize_PCA)
export(TCGAvisualize_SurvivalCoxNET)
export(TCGAvisualize_meanMethylation)
export(TCGAvisualize_oncoprint)
export(TCGAvisualize_starburst)
export(UseRaw_afterFilter)
export(gaiaCNVplot)
export(getAdjacencyBiogrid)
export(getDataCategorySummary)
export(getGDCInfo)
export(getGDCprojects)
export(getGistic)
export(getManifest)
export(getResults)
export(get_IDs)
export(isServeOK)
export(matchedMetExp)
import(ComplexHeatmap)
import(GenomeInfoDb)
import(ggplot2)
import(graphics)
import(httr)
import(readr)
import(selectr)
import(stats)
import(stringr)
import(utils)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,oncoPrint)
importFrom(ConsensusClusterPlus,ConsensusClusterPlus)
importFrom(EDASeq,barplot)
importFrom(EDASeq,betweenLaneNormalization)
importFrom(EDASeq,counts)
importFrom(EDASeq,exprs)
importFrom(EDASeq,newSeqExpressionSet)
importFrom(EDASeq,offst)
importFrom(EDASeq,withinLaneNormalization)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,distanceToNearest)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,promoters)
importFrom(IRanges,IRanges)
importFrom(R.utils,gunzip)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,values)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"metadata<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,"values<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(XML,getNodeSet)
importFrom(XML,xmlParse)
importFrom(XML,xmlToDataFrame)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,useEnsembl)
importFrom(biomaRt,useMart)
importFrom(circlize,colorRamp2)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,dcast)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(data.table,setDF)
importFrom(data.table,setDT)
importFrom(data.table,setcolorder)
importFrom(data.table,setnames)
importFrom(doParallel,registerDoParallel)
importFrom(downloader,download)
importFrom(dplyr,data_frame)
importFrom(dplyr,funs)
importFrom(dplyr,mutate_all)
importFrom(edgeR,DGEList)
importFrom(edgeR,estimateCommonDisp)
importFrom(edgeR,estimateGLMCommonDisp)
importFrom(edgeR,estimateGLMTagwiseDisp)
importFrom(edgeR,exactTest)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(genefilter,varFilter)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(ggthemes,theme_base)
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(grid,gpar)
importFrom(grid,grid.rect)
importFrom(gridExtra,gtable_rbind)
importFrom(httr,content)
importFrom(httr,timeout)
importFrom(jsonlite,fromJSON)
importFrom(knitr,kable)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,toptable)
importFrom(limma,voom)
importFrom(matlab,jet.colors)
importFrom(methods,as)
importFrom(methods,is)
importFrom(parallel,detectCores)
importFrom(plyr,.)
importFrom(plyr,adply)
importFrom(plyr,ddply)
importFrom(plyr,rbind.fill)
importFrom(plyr,summarize)
importFrom(rvest,"%>%")
importFrom(rvest,html_attr)
importFrom(rvest,html_nodes)
importFrom(scales,muted)
importFrom(scales,percent)
importFrom(stats,wilcox.test)
importFrom(stats,xtabs)
importFrom(survival,Surv)
importFrom(survival,coxph)
importFrom(survival,survdiff)
importFrom(survival,survfit)
importFrom(survminer,ggsurvplot)
importFrom(sva,ComBat)
importFrom(tibble,as_data_frame)
importFrom(tools,file_ext)
importFrom(tools,md5sum)
importFrom(utils,untar)
importFrom(xml2,read_html)
importFrom(xml2,read_xml)
importFrom(xml2,xml_ns)
