# Generated by roxygen2: do not edit by hand

export(GDCdownload)
export(GDCprepare)
export(GDCprepare_clinic)
export(GDCquery)
export(GDCquery_ATAC_seq)
export(GDCquery_clinic)
export(PanCancerAtlas_subtypes)
export(TCGAVisualize_volcano)
export(TCGA_MolecularSubtype)
export(TCGAanalyze_Clustering)
export(TCGAanalyze_DEA)
export(TCGAanalyze_DEA_Affy)
export(TCGAanalyze_DMC)
export(TCGAanalyze_EAcomplete)
export(TCGAanalyze_Filtering)
export(TCGAanalyze_LevelTab)
export(TCGAanalyze_Normalization)
export(TCGAanalyze_Pathview)
export(TCGAanalyze_Preprocessing)
export(TCGAanalyze_Stemness)
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(colDataPrepare)
export(gaiaCNVplot)
export(get.GRCh.bioMart)
export(getAdjacencyBiogrid)
export(getDataCategorySummary)
export(getGDCInfo)
export(getGDCprojects)
export(getGistic)
export(getLinkedOmicsData)
export(getMC3MAF)
export(getManifest)
export(getProjectSummary)
export(getResults)
export(getSampleFilesSummary)
export(get_IDs)
export(gliomaClassifier)
export(isServeOK)
export(matchedMetExp)
import(TCGAbiolinksGUI.data)
import(ggplot2)
import(graphics)
import(httr)
import(readr)
import(stats)
import(stringr)
import(utils)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,distanceToNearest)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,promoters)
importFrom(IRanges,IRanges)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
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(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(downloader,download)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,data_frame)
importFrom(dplyr,funs)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate_all)
importFrom(dplyr,pull)
importFrom(dplyr,row_number)
importFrom(dplyr,slice)
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(httr,content)
importFrom(httr,timeout)
importFrom(jsonlite,fromJSON)
importFrom(knitr,kable)
importFrom(methods,as)
importFrom(methods,is)
importFrom(plyr,.)
importFrom(plyr,adply)
importFrom(plyr,alply)
importFrom(plyr,count)
importFrom(plyr,ddply)
importFrom(plyr,join_all)
importFrom(plyr,ldply)
importFrom(plyr,rbind.fill)
importFrom(plyr,summarize)
importFrom(purrr,map)
importFrom(purrr,map2_dfr)
importFrom(purrr,map_chr)
importFrom(purrr,map_df)
importFrom(purrr,map_dfc)
importFrom(rvest,"%>%")
importFrom(rvest,html_attr)
importFrom(rvest,html_nodes)
importFrom(stats,wilcox.test)
importFrom(stats,xtabs)
importFrom(stringr,str_c)
importFrom(tibble,as_data_frame)
importFrom(tidyr,contains)
importFrom(tidyr,separate)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(tools,md5sum)
importFrom(utils,untar)
importFrom(xml2,read_html)
importFrom(xml2,read_xml)
importFrom(xml2,xml_ns)
