| c3b84cf0 |
# Generated by roxygen2: do not edit by hand
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| cf2ebdfb |
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| bfd9e470 |
S3method(print,header)
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| 06f6f2b0 |
export(GDCdownload)
export(GDCprepare)
export(GDCprepare_clinic)
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| 178c3b9a |
export(GDCquery)
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| ffb24e8d |
export(GDCquery_ATAC_seq)
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| 178c3b9a |
export(GDCquery_clinic)
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| 22ab6610 |
export(PanCancerAtlas_subtypes)
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| f32ada09 |
export(TCGAVisualize_volcano)
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| ddb89f51 |
export(TCGA_MolecularSubtype)
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| f32ada09 |
export(TCGAanalyze_Clustering)
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| cf2ebdfb |
export(TCGAanalyze_DEA)
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| f32ada09 |
export(TCGAanalyze_DEA_Affy)
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| 7f8b8e4b |
export(TCGAanalyze_DMC)
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| cf2ebdfb |
export(TCGAanalyze_EAcomplete)
export(TCGAanalyze_Filtering)
export(TCGAanalyze_LevelTab)
export(TCGAanalyze_Normalization)
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| 5561a826 |
export(TCGAanalyze_Pathview)
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| cf2ebdfb |
export(TCGAanalyze_Preprocessing)
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| 70d1b5c5 |
export(TCGAanalyze_Stemness)
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| cf2ebdfb |
export(TCGAanalyze_SurvivalKM)
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| a8002763 |
export(TCGAanalyze_analyseGRN)
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| 5b7bc833 |
export(TCGAanalyze_networkInference)
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| cf2ebdfb |
export(TCGAanalyze_survival)
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| 473d1bda |
export(TCGAbatch_Correction)
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| f32ada09 |
export(TCGAprepare_Affy)
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| cf2ebdfb |
export(TCGAquery_MatchedCoupledSampleTypes)
export(TCGAquery_SampleTypes)
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| 473d1bda |
export(TCGAquery_recount2)
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| d1d85ee4 |
export(TCGAquery_subtype)
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| 473d1bda |
export(TCGAtumor_purity)
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| cb8583c7 |
export(TCGAvisualize_BarPlot)
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| cf2ebdfb |
export(TCGAvisualize_EAbarplot)
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| f32ada09 |
export(TCGAvisualize_Heatmap)
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| cf2ebdfb |
export(TCGAvisualize_PCA)
export(TCGAvisualize_meanMethylation)
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| 79de3b6c |
export(TCGAvisualize_oncoprint)
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| cf2ebdfb |
export(TCGAvisualize_starburst)
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| 473d1bda |
export(UseRaw_afterFilter)
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| a3f2bc5f |
export(colDataPrepare)
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| 7ac30a54 |
export(gaiaCNVplot)
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| a3f2bc5f |
export(get.GRCh.bioMart)
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| 7ac30a54 |
export(getAdjacencyBiogrid)
export(getDataCategorySummary)
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| 8208b681 |
export(getGDCInfo)
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| 178c3b9a |
export(getGDCprojects)
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| 1b53269a |
export(getGistic)
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| baf84f8c |
export(getLinkedOmicsData)
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| 9bd9c765 |
export(getMC3MAF)
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| 1692d5bd |
export(getManifest)
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| ed005a2a |
export(getProjectSummary)
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| 32d7435e |
export(getResults)
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| 222b73fc |
export(getSampleFilesSummary)
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| fdff3742 |
export(get_IDs)
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| b756404e |
export(gliomaClassifier)
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| 178c3b9a |
export(isServeOK)
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| 7ac30a54 |
export(matchedMetExp)
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| 18fd2879 |
import(TCGAbiolinksGUI.data)
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| cf2ebdfb |
import(ggplot2)
import(graphics)
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| 9d364efb |
import(httr)
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| 178c3b9a |
import(readr)
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| cf2ebdfb |
import(stats)
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| 178c3b9a |
import(stringr)
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| cf2ebdfb |
import(utils)
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| 9a62fdd6 |
importFrom(GenomicRanges,GRanges)
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| 0a55b48a |
importFrom(GenomicRanges,distanceToNearest)
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| 0d7a13b9 |
importFrom(GenomicRanges,makeGRangesFromDataFrame)
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| 0961a047 |
importFrom(GenomicRanges,promoters)
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| 9a62fdd6 |
importFrom(IRanges,IRanges)
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| ee9a77b7 |
importFrom(S4Vectors,DataFrame)
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| d1d85ee4 |
importFrom(S4Vectors,metadata)
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| 0a55b48a |
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
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| cf2ebdfb |
importFrom(SummarizedExperiment,"colData<-")
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| ee9a77b7 |
importFrom(SummarizedExperiment,"metadata<-")
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| cf2ebdfb |
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,"values<-")
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| ee9a77b7 |
importFrom(SummarizedExperiment,SummarizedExperiment)
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| cf2ebdfb |
importFrom(SummarizedExperiment,assay)
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| 31adc846 |
importFrom(SummarizedExperiment,assays)
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| cf2ebdfb |
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
|
| 04adb143 |
importFrom(XML,getNodeSet)
importFrom(XML,xmlParse)
importFrom(XML,xmlToDataFrame)
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| 7b305766 |
importFrom(biomaRt,getBM)
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| afcb2a28 |
importFrom(biomaRt,listDatasets)
|
| 5e8c1cce |
importFrom(biomaRt,useEnsembl)
|
| 79de3b6c |
importFrom(data.table,":=")
|
| 93f667c9 |
importFrom(data.table,as.data.table)
|
| 79de3b6c |
importFrom(data.table,dcast)
|
| 7fe66781 |
importFrom(data.table,fread)
|
| 178c3b9a |
importFrom(data.table,rbindlist)
|
| c3b84cf0 |
importFrom(data.table,setDF)
|
| 79de3b6c |
importFrom(data.table,setDT)
|
| eba132ca |
importFrom(data.table,setcolorder)
importFrom(data.table,setnames)
|
| cf2ebdfb |
importFrom(downloader,download)
|
| c1e5918e |
importFrom(dplyr,bind_cols)
|
| 5d5bf886 |
importFrom(dplyr,bind_rows)
|
| f32ada09 |
importFrom(dplyr,data_frame)
|
| 87f927d8 |
importFrom(dplyr,funs)
|
| 6bf60949 |
importFrom(dplyr,left_join)
|
| b5ebdda4 |
importFrom(dplyr,mutate_all)
|
| e0a24d6d |
importFrom(dplyr,pull)
|
| eb4267de |
importFrom(dplyr,row_number)
importFrom(dplyr,slice)
|
| b2bc706f |
importFrom(dplyr,summarise)
|
| cf2ebdfb |
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
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| d1d85ee4 |
importFrom(grDevices,rainbow)
|
| 7ac30a54 |
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,plot)
importFrom(graphics,points)
|
| 008efdf3 |
importFrom(httr,content)
|
| 530775ea |
importFrom(httr,timeout)
|
| 178c3b9a |
importFrom(jsonlite,fromJSON)
|
| 09923d64 |
importFrom(knitr,kable)
|
| b565f8b3 |
importFrom(methods,as)
|
| 68de40aa |
importFrom(methods,is)
|
| 88e0f72e |
importFrom(plyr,.)
|
| d1d85ee4 |
importFrom(plyr,adply)
|
| 1ad91a9b |
importFrom(plyr,alply)
|
| 80cc6161 |
importFrom(plyr,count)
|
| cf2ebdfb |
importFrom(plyr,ddply)
|
| d7615b50 |
importFrom(plyr,join_all)
|
| 46084669 |
importFrom(plyr,ldply)
|
| e300cffe |
importFrom(plyr,rbind.fill)
|
| 70397001 |
importFrom(plyr,summarize)
|
| 6d660137 |
importFrom(purrr,map)
|
| 53d3835c |
importFrom(purrr,map2_dfr)
|
| 28ae53ec |
importFrom(purrr,map_chr)
|
| dbee506d |
importFrom(purrr,map_df)
|
| 8b8a1b98 |
importFrom(purrr,map_dfc)
|
| 6dcc778d |
importFrom(rvest,"%>%")
|
| 2d421843 |
importFrom(rvest,html_attr)
importFrom(rvest,html_nodes)
|
| f8e725fe |
importFrom(stats,wilcox.test)
|
| f631552d |
importFrom(stats,xtabs)
|
| acdc3fa8 |
importFrom(stringr,str_c)
|
| 0d7a13b9 |
importFrom(tibble,as_data_frame)
|
| afcb2a28 |
importFrom(tidyr,contains)
|
| 9e56ad43 |
importFrom(tidyr,separate)
|
| 80cc6161 |
importFrom(tidyr,spread)
importFrom(tidyr,unite)
|
| 178c3b9a |
importFrom(tools,md5sum)
|
| 95f473a5 |
importFrom(utils,untar)
|
| 2d421843 |
importFrom(xml2,read_html)
|
| 04adb143 |
importFrom(xml2,read_xml)
importFrom(xml2,xml_ns)
|
